FightAIDS@Home

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Project Status, page 1, as of December 5, 2013

As of July 18, 2013, some FightAIDS@Home experiments will now use the software "AutoDock Vina" (or "AD Vina"). See https://secure.worldcommunitygrid.org/forums/wcg/viewthread_thread,35382 for more information.

Note: one "batch" with AutoDock involves docking ~ 1,000 compounds, while one "batch" with AD Vina involves docking ~ 10,000 compounds.

Experiments 121 to 126 (AD Vina), 0% completed

Experiments 121 through 126 target the active site of HIV protease. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge. These experiments will help determine the differences and utility of varying the dimensions of a "docking box." The focus of these experiments is on the allosteric sites of HIV protease.

*TARGET: exterior sites of PR*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 121 AD Vina Exp. 67	AD Exp. 122 AD Vina Exp. 68	AD Exp. 123 AD Vina Exp. 69	AD Exp. 124 AD Vina Exp. 70	AD Exp. 125 AD Vina Exp. 71	AD Exp. 126 AD Vina Exp. 72
PDB 1ZTZ, Exterior Sites, Side 1	552395-552426	553227-553461	559337-559438	561989-562039	563315-563465	567241-567248
PDB 1ZTZ, Exterior Sites, Side 2	552427-552458	553462-553696	559439-559540	562040-562090	563466-563616	567249-567256
PDB 3I8Wa, Exterior Sites, Side 1	552459-552490	553697-553931	559541-559642	562091-562141	563617-563767	567257-567264
PDB 3I8Wa, Exterior Sites, Side 2	552491-552522	553932-554166	559643-559744	562142-562192	563768-563918	567265-567272
PDB 3I8Wb, Exterior Sites, Side 1	552523-552554	554167-554401	559745-559846	562193-562243	563919-564069	567273-567280
PDB 3I8Wb, Exterior Sites, Side 2	552555-552586	554402-554636	559847-559948	562244-562294	564070-564220	567281-567288
PDB 3KF0, Exterior Sites, Side 1	552587-552618	554637-554871	559949-560050	562295-562345	564221-564371	567289-567296
PDB 3KF0, Exterior Sites, Side 2	552619-552650	554872-555106	560051-560152	562346-562396	564372-564522	567297-567304
PDB 3KFN, Exterior Sites, Side 1	552651-552682	555107-555341	560153-560254	562397-562447	564523-564673	567305-567312
PDB 3KFN, Exterior Sites, Side 2	552683-552714	555342-555576	560255-560356	562448-562498	564674-564824	567313-567320
PDB 3KFP, Exterior Sites, Side 1	552715-552746	555577-555811	560357-560458	562499-562549	564825-564975	567321-567328
PDB 3KFP, Exterior Sites, Side 2	552747-552778	555812-556046	560459-560560	562550-562600	564976-565126	567329-567336
PDB 3KFR, Exterior Sites, Side 1	552779-552810	556047-556281	560561-560662	562601-562651	565127-565277	567337-567344
PDB 3KFR, Exterior Sites, Side 2	552811-552842	556282-556516	560663-560764	562652-562702	565278-565428	567345-567352
PDB 3KFS, Exterior Sites, Side 1	552843-552874	556517-556751	560765-560866	562703-562753	565429-565579	567353-567360
PDB 3KFS, Exterior Sites, Side 2	552875-552906	556752-556986	560867-560968	562754-562804	565580-565730	567361-567368
PDB 3T11a, Exterior Sites, Side 1	552907-552938	556987-557221	560969-561070	562805-562855	565731-565881	567369-567376
PDB 3T11a, Exterior Sites, Side 2	552939-552970	557222-557456	561071-561172	562856-562906	565882-566032	567377-567384
PDB 3T11b, Exterior Sites, Side 1	552971-553002	557457-557691	561173-561274	562907-562957	566033-566183	567385-567392
PDB 3T11b, Exterior Sites, Side 2	553003-553034	557692-557926	561275-561376	562958-563008	566184-566334	567393-567400
PDB 4DQG, Exterior Sites, Side 1	553035-553066	557927-558161	561377-561478	563009-563059	566335-566485	567401-567408
PDB 4DQG, Exterior Sites, Side 2	553067-553098	558162-558396	561479-561580	563060-563110	566486-566636	567409-567416
PDB 4E43a, Exterior Sites, Side 1	553099-553130	558397-558631	561581-561682	563111-563161	566637-566787	567417-567424
PDB 4E43a, Exterior Sites, Side 2	553131-553162	558632-558866	561683-561784	563162-563212	566788-566938	567425-567432
PDB 4E43b, Exterior Sites, Side 1	553163-553194	558867-559101	561785-561886	563213-563263	566939-567089	567433-567440
PDB 4E43b, Exterior Sites, Side 2	553195-553226	559102-559336	561887-561988	563264-563314	567090-567240	567441-567448
COMPLETION	0%	0%	0%	0%	0%	0%

Experiments 115 to 120 (AD Vina), 0% completed

Experiments 115 through 120 target the active site of HIV protease. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge. These experiments will help distinguish better sites of among a group of receptor structures even within the same structure. Potentially important molecules (in these cases: water and/or chloride ion) found in the original structures are left in different combinations to produce varied models for HIV protease.

*TARGET: active site of PR*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 115 AD Vina Exp. 61	AD Exp. 116 AD Vina Exp. 62	AD Exp. 117 AD Vina Exp. 63	AD Exp. 118 AD Vina Exp. 64	AD Exp. 119 AD Vina Exp. 65	AD Exp. 120 AD Vina Exp. 66
PDB 1ZTZ, Active Site	396767-396798	405326-405560	468641-468742	496019-496069	509708-509858	550316-550323
PDB 3I8Wa, Active Site	396799-396830	405561-405795	468743-468844	496070-496120	509859-510009	550324-550331
PDB 3I8Wb, Active Site	396831-396862	405796-406030	468845-468946	496121-496171	510010-510160	550332-550339
PDB 3KF0, Active Site	396863-396894	406031-406265	468947-469048	496172-496222	510161-510311	550340-550347
PDB 3KF0 with water, Active Site	396895-396926	406266-406500	469049-469150	496223-496273	510312-510462	550348-550355
PDB 3KFN, Active Site	396927-396958	406501-406735	469151-469252	496274-496324	510463-510613	550356-550363
PDB 3KFN with water, Active Site	396959-396990	406736-406970	469253-469354	496325-496375	510614-510764	550364-550371
PDB 3KFP, Active Site	396991-397022	406971-407205	469355-469456	496376-496426	510765-510915	550372-550379
PDB 3KFP with water, Active Site	397023-397054	407206-407440	469457-469558	496427-496477	510916-511066	550380-550387
PDB 3KFR, Active Site	397055-397086	407441-407675	469559-469660	496478-496528	511067-511217	550388-550395
PDB 3KFR with water, Active Site	397087-397118	407676-407910	469661-469762	496529-496579	511218-511368	550396-550403
PDB 3KFS, Active Site	397119-397150	407911-408145	469763-469864	496580-496630	511369-511519	550404-550411
PDB 3KFS with water, Active Site	397151-397182	408146-408380	469865-469966	496631-496681	511520-511670	550412-550419
PDB 3T11a, Active Site	397183-397214	408381-408615	469967-470068	496682-496732	511671-511821	550420-550427
PDB 3T11a with chloride, Active Site	397215-397246	408616-408850	470069-470170	496733-496783	511822-511972	550428-550435
PDB 3T11a with water, Active Site	397247-397278	408851-409085	470171-470272	496784-496834	511973-512123	550436-550443
PDB 3T11a with chloride and water, Active Site	397279-397310	409086-409320	470273-470374	496835-496885	512124-512274	550444-550451
PDB 3T11b, Active Site	397311-397342	409321-409555	470375-470476	496886-496936	512275-512425	550452-550459
PDB 3T11b with chloride, Active Site	397343-397374	409556-409790	470477-470578	496937-496987	512426-512576	550460-550467
PDB 3T11b with water, Active Site	397375-397406	409791-410025	470579-470680	496988-497038	512577-512727	550468-550475
PDB 3T11b with chloride and water, Active Site	397407-397438	410026-410260	470681-470782	497039-497089	512728-512878	550476-550483
PDB 4DQG, Active Site	397439-397470	410261-410495	470783-470884	497090-497140	512879-513029	550484-550491
PDB 4DQG with water, Active Site	397471-397502	410496-410730	470885-470986	497141-497191	513030-513180	550492-550499
PDB 4E43a, Active Site	397503-397534	410731-410965	470987-471088	497192-497242	513181-513331	550500-550507
PDB 4E43a with water, Active Site	397535-397566	410966-411200	471089-471190	497243-497293	513332-513482	550508-550515
PDB 4E43b, Active Site	397567-397598	411201-411435	471191-471292	497294-497344	513483-513633	550516-550523
PDB 4E43b with water, Active Site	397599-397630	411436-411670	471293-471394	497345-497395	513634-513784	550524-550531
COMPLETION	0%	0%	0%	0%	0%	0%

Experiments 109 to 114 (AutoDock), 0% completed

Experiments 109 through 114 target the LEDGF site of HIV integrase. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge. These experiments will help distinguish better sites of among a group of receptor structures even within the same structure. To help read structures in the table below, the "a" and "b" after the 4-character PDB ID designate those receptor structures with alternate residue positions, while the "a" and "b" with the sites (FBP, LEDGF, Y3) designate different sites for the same symmetric structure of HIV IN.

*TARGET: LEDGFa Site of HIV Integrase*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 109	AD Exp. 110	AD Exp. 111	AD Exp. 112	AD Exp. 113	AD Exp. 114
PDB 4GVMa, LEDGFa Site	374019-374335	381371-383715	377315-378328	375287-375793	390751-392254	373711-373787
PDB 4GVMb, LEDGFa Site	374336-374652	383716-386060	378329-379342	375794-376300	392255-393758	373788-373864
PDB 4GW6a, LEDGFa Site	374653-374969	386061-388405	379343-380356	376301-376807	393759-395262	373865-373941
PDB 4GW6b, LEDGFa Site	374970-375286	388406-390750	380357-381370	376808-377314	395263-396766	373942-374018
COMPLETION	0%	0%	0%	0%	0%	0%

Experiments 103 to 108 (AD Vina), 1% completed

Experiments 103 through 108 target allosteric sites of HIV integrase (FBP, LEDGF, and Y3 (under the 140s residues loop) sites). These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge with AD Vina against various (receptor) structures from the PDB. These experiments complement Experiments 47 - 51, 91 - 96; however, these experiments will help distinguish better sites of among a group of receptor structures even within the same structure. For example, the HIV receptor structure containing the allosteric sites actually contains 2 sites for each of FBP, LEDGF, and Y3 pockets due to the symmetric nature of the HIV IN catalytic core domain (CCD). To help read structures in the table below, the "a" and "b" after the 4-character PDB ID designate those receptor structures with alternate residue positions, while the "a" and "b" with the sites (FBP, LEDGF, Y3) designate different sites for the same symmetric structure of HIV IN.

*TARGET: FBP, LEDGF, and ,Y3 Sites of HIV Integrase*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 103 AD Vina Exp. 55	AD Exp. 104 AD Vina Exp. 56	AD Exp. 105 AD Vina Exp. 57	AD Exp. 106 AD Vina Exp. 58	AD Exp. 107 AD Vina Exp. 59	AD Exp. 108 AD Vina Exp. 60
PDB 3AV9a, FBPa Site	281071-281102	286191-286425	323791-323892	340111-340161	348271-348421	372431-372438
PDB 3AV9a, FBPb Site	281103-281134	286426-286660	323893-323994	340162-340212	348422-348572	372439-372446
PDB 3AV9a, LEDGFa Site	281135-281166	286661-286895	323995-324096	340213-340263	348573-348723	372447-372454
PDB 3AV9a, LEDGFb Site	281167-281198	286896-287130	324097-324198	340264-340314	348724-348874	372455-372462
PDB 3AV9a, Y3a Site	281199-281230	287131-287365	324199-324300	340315-340365	348875-349025	372463-372470
PDB 3AV9a, Y3b Site	281231-281262	287366-287600	324301-324402	340366-340416	349026-349176	372471-372478
PDB 3AV9b, FBPa Site	281263-281294	287601-287835	324403-324504	340417-340467	349177-349327	372479-372486
PDB 3AV9b, FBPb Site	281295-281326	287836-288070	324505-324606	340468-340518	349328-349478	372487-372494
PDB 3AV9b, LEDGFa Site	281327-281358	288071-288305	324607-324708	340519-340569	349479-349629	372495-372502
PDB 3AV9b, LEDGFb Site	281359-281390	288306-288540	324709-324810	340570-340620	349630-349780	372503-372510
PDB 3AV9b, Y3a Site	281391-281422	288541-288775	324811-324912	340621-340671	349781-349931	372511-372518
PDB 3AV9b, Y3b Site	281423-281454	288776-289010	324913-325014	340672-340722	349932-350082	372519-372526
PDB 3AVAa, FBPa Site	281455-281486	289011-289245	325015-325116	340723-340773	350083-350233	372527-372534
PDB 3AVAa, FBPb Site	281487-281518	289246-289480	325117-325218	340774-340824	350234-350384	372535-372542
PDB 3AVAa, LEDGFa Site	281519-281550	289481-289715	325219-325320	340825-340875	350385-350535	372543-372550
PDB 3AVAa, LEDGFb Site	281551-281582	289716-289950	325321-325422	340876-340926	350536-350686	372551-372558
PDB 3AVAa, Y3a Site	281583-281614	289951-290185	325423-325524	340927-340977	350687-350837	372559-372566
PDB 3AVAa, Y3b Site	281615-281646	290186-290420	325525-325626	340978-341028	350838-350988	372567-372574
PDB 3AVAb, FBPa Site	281647-281678	290421-290655	325627-325728	341029-341079	350989-351139	372575-372582
PDB 3AVAb, FBPb Site	281679-281710	290656-290890	325729-325830	341080-341130	351140-351290	372583-372590
PDB 3AVAb, LEDGFa Site	281711-281742	290891-291125	325831-325932	341131-341181	351291-351441	372591-372598
PDB 3AVAb, LEDGFb Site	281743-281774	291126-291360	325933-326034	341182-341232	351442-351592	372599-372606
PDB 3AVAb, Y3a Site	281775-281806	291361-291595	326035-326136	341233-341283	351593-351743	372607-372614
PDB 3AVAb, Y3b Site	281807-281838	291596-291830	326137-326238	341284-341334	351744-351894	372615-372622
PDB 3AVCa, FBPa Site	281839-281870	291831-292065	326239-326340	341335-341385	351895-352045	372623-372630
PDB 3AVCa, FBPb Site	281871-281902	292066-292300	326341-326442	341386-341436	352046-352196	372631-372638
PDB 3AVCa, LEDGFa Site	281903-281934	292301-292535	326443-326544	341437-341487	352197-352347	372639-372646
PDB 3AVCa, LEDGFb Site	281935-281966	292536-292770	326545-326646	341488-341538	352348-352498	372647-372654
PDB 3AVCa, Y3a Site	281967-281998	292771-293005	326647-326748	341539-341589	352499-352649	372655-372662
PDB 3AVCa, Y3b Site	281999-282030	293006-293240	326749-326850	341590-341640	352650-352800	372663-372670
PDB 3AVCb, FBPa Site	282031-282062	293241-293475	326851-326952	341641-341691	352801-352951	372671-372678
PDB 3AVCb, FBPb Site	282063-282094	293476-293710	326953-327054	341692-341742	352952-353102	372679-372686
PDB 3AVCb, LEDGFa Site	282095-282126	293711-293945	327055-327156	341743-341793	353103-353253	372687-372694
PDB 3AVCb, LEDGFb Site	282127-282158	293946-294180	327157-327258	341794-341844	353254-353404	372695-372702
PDB 3AVCb, Y3a Site	282159-282190	294181-294415	327259-327360	341845-341895	353405-353555	372703-372710
PDB 3AVCb, Y3b Site	282191-282222	294416-294650	327361-327462	341896-341946	353556-353706	372711-372718
PDB 3AVFa, FBPa Site	282223-282254	294651-294885	327463-327564	341947-341997	353707-353857	372719-372726
PDB 3AVFa, FBPb Site	282255-282286	294886-295120	327565-327666	341998-342048	353858-354008	372727-372734
PDB 3AVFa, LEDGFa Site	282287-282318	295121-295355	327667-327768	342049-342099	354009-354159	372735-372742
PDB 3AVFa, LEDGFb Site	282319-282350	295356-295590	327769-327870	342100-342150	354160-354310	372743-372750
PDB 3AVFa, Y3a Site	282351-282382	295591-295825	327871-327972	342151-342201	354311-354461	372751-372758
PDB 3AVFa, Y3b Site	282383-282414	295826-296060	327973-328074	342202-342252	354462-354612	372759-372766
PDB 3AVFb, FBPa Site	282415-282446	296061-296295	328075-328176	342253-342303	354613-354763	372767-372774
PDB 3AVFb, FBPb Site	282447-282478	296296-296530	328177-328278	342304-342354	354764-354914	372775-372782
PDB 3AVFb, LEDGFa Site	282479-282510	296531-296765	328279-328380	342355-342405	354915-355065	372783-372790
PDB 3AVFb, LEDGFb Site	282511-282542	296766-297000	328381-328482	342406-342456	355066-355216	372791-372798
PDB 3AVFb, Y3a Site	282543-282574	297001-297235	328483-328584	342457-342507	355217-355367	372799-372806
PDB 3AVFb, Y3b Site	282575-282606	297236-297470	328585-328686	342508-342558	355368-355518	372807-372814
PDB 3AVGa, FBPa Site	282607-282638	297471-297705	328687-328788	342559-342609	355519-355669	372815-372822
PDB 3AVGa, FBPb Site	282639-282670	297706-297940	328789-328890	342610-342660	355670-355820	372823-372830
PDB 3AVGa, LEDGFa Site	282671-282702	297941-298175	328891-328992	342661-342711	355821-355971	372831-372838
PDB 3AVGa, LEDGFb Site	282703-282734	298176-298410	328993-329094	342712-342762	355972-356122	372839-372846
PDB 3AVGa, Y3a Site	282735-282766	298411-298645	329095-329196	342763-342813	356123-356273	372847-372854
PDB 3AVGa, Y3b Site	282767-282798	298646-298880	329197-329298	342814-342864	356274-356424	372855-372862
PDB 3AVGb, FBPa Site	282799-282830	298881-299115	329299-329400	342865-342915	356425-356575	372863-372870
PDB 3AVGb, FBPb Site	282831-282862	299116-299350	329401-329502	342916-342966	356576-356726	372871-372878
PDB 3AVGb, LEDGFa Site	282863-282894	299351-299585	329503-329604	342967-343017	356727-356877	372879-372886
PDB 3AVGb, LEDGFb Site	282895-282926	299586-299820	329605-329706	343018-343068	356878-357028	372887-372894
PDB 3AVGb, Y3a Site	282927-282958	299821-300055	329707-329808	343069-343119	357029-357179	372895-372902
PDB 3AVGb, Y3b Site	282959-282990	300056-300290	329809-329910	343120-343170	357180-357330	372903-372910
PDB 3AVHa, FBPa Site	282991-283022	300291-300525	329911-330012	343171-343221	357331-357481	372911-372918
PDB 3AVHa, FBPb Site	283023-283054	300526-300760	330013-330114	343222-343272	357482-357632	372919-372926
PDB 3AVHa, LEDGFa Site	283055-283086	300761-300995	330115-330216	343273-343323	357633-357783	372927-372934
PDB 3AVHa, LEDGFb Site	283087-283118	300996-301230	330217-330318	343324-343374	357784-357934	372935-372942
PDB 3AVHa, Y3a Site	283119-283150	301231-301465	330319-330420	343375-343425	357935-358085	372943-372950
PDB 3AVHa, Y3b Site	283151-283182	301466-301700	330421-330522	343426-343476	358086-358236	372951-372958
PDB 3AVHb, FBPa Site	283183-283214	301701-301935	330523-330624	343477-343527	358237-358387	372959-372966
PDB 3AVHb, FBPb Site	283215-283246	301936-302170	330625-330726	343528-343578	358388-358538	372967-372974
PDB 3AVHb, LEDGFa Site	283247-283278	302171-302405	330727-330828	343579-343629	358539-358689	372975-372982
PDB 3AVHb, LEDGFb Site	283279-283310	302406-302640	330829-330930	343630-343680	358690-358840	372983-372990
PDB 3AVHb, Y3a Site	283311-283342	302641-302875	330931-331032	343681-343731	358841-358991	372991-372998
PDB 3AVHb, Y3b Site	283343-283374	302876-303110	331033-331134	343732-343782	358992-359142	372999-373006
PDB 3AVIa, FBPa Site	283375-283406	303111-303345	331135-331236	343783-343833	359143-359293	373007-373014
PDB 3AVIa, FBPb Site	283407-283438	303346-303580	331237-331338	343834-343884	359294-359444	373015-373022
PDB 3AVIa, LEDGFa Site	283439-283470	303581-303815	331339-331440	343885-343935	359445-359595	373023-373030
PDB 3AVIa, LEDGFb Site	283471-283502	303816-304050	331441-331542	343936-343986	359596-359746	373031-373038
PDB 3AVIa, Y3a Site	283503-283534	304051-304285	331543-331644	343987-344037	359747-359897	373039-373046
PDB 3AVIa, Y3b Site	283535-283566	304286-304520	331645-331746	344038-344088	359898-360048	373047-373054
PDB 3AVIb, FBPa Site	283567-283598	304521-304755	331747-331848	344089-344139	360049-360199	373055-373062
PDB 3AVIb, FBPb Site	283599-283630	304756-304990	331849-331950	344140-344190	360200-360350	373063-373070
PDB 3AVIb, LEDGFa Site	283631-283662	304991-305225	331951-332052	344191-344241	360351-360501	373071-373078
PDB 3AVIb, LEDGFb Site	283663-283694	305226-305460	332053-332154	344242-344292	360502-360652	373079-373086
PDB 3AVIb, Y3a Site	283695-283726	305461-305695	332155-332256	344293-344343	360653-360803	373087-373094
PDB 3AVIb, Y3b Site	283727-283758	305696-305930	332257-332358	344344-344394	360804-360954	373095-373102
PDB 3AVJa, FBPa Site	283759-283790	305931-306165	332359-332460	344395-344445	360955-361105	373103-373110
PDB 3AVJa, FBPb Site	283791-283822	306166-306400	332461-332562	344446-344496	361106-361256	373111-373118
PDB 3AVJa, LEDGFa Site	283823-283854	306401-306635	332563-332664	344497-344547	361257-361407	373119-373126
PDB 3AVJa, LEDGFb Site	283855-283886	306636-306870	332665-332766	344548-344598	361408-361558	373127-373134
PDB 3AVJa, Y3a Site	283887-283918	306871-307105	332767-332868	344599-344649	361559-361709	373135-373142
PDB 3AVJa, Y3b Site	283919-283950	307106-307340	332869-332970	344650-344700	361710-361860	373143-373150
PDB 3AVJb, FBPa Site	283951-283982	307341-307575	332971-333072	344701-344751	361861-362011	373151-373158
PDB 3AVJb, FBPb Site	283983-284014	307576-307810	333073-333174	344752-344802	362012-362162	373159-373166
PDB 3AVJb, LEDGFa Site	284015-284046	307811-308045	333175-333276	344803-344853	362163-362313	373167-373174
PDB 3AVJb, LEDGFb Site	284047-284078	308046-308280	333277-333378	344854-344904	362314-362464	373175-373182
PDB 3AVJb, Y3a Site	284079-284110	308281-308515	333379-333480	344905-344955	362465-362615	373183-373190
PDB 3AVJb, Y3b Site	284111-284142	308516-308750	333481-333582	344956-345006	362616-362766	373191-373198
PDB 3AVKa, FBPa Site	284143-284174	308751-308985	333583-333684	345007-345057	362767-362917	373199-373206
PDB 3AVKa, FBPb Site	284175-284206	308986-309220	333685-333786	345058-345108	362918-363068	373207-373214
PDB 3AVKa, LEDGFa Site	284207-284238	309221-309455	333787-333888	345109-345159	363069-363219	373215-373222
PDB 3AVKa, LEDGFb Site	284239-284270	309456-309690	333889-333990	345160-345210	363220-363370	373223-373230
PDB 3AVKa, Y3a Site	284271-284302	309691-309925	333991-334092	345211-345261	363371-363521	373231-373238
PDB 3AVKa, Y3b Site	284303-284334	309926-310160	334093-334194	345262-345312	363522-363672	373239-373246
PDB 3AVKb, FBPa Site	284335-284366	310161-310395	334195-334296	345313-345363	363673-363823	373247-373254
PDB 3AVKb, FBPb Site	284367-284398	310396-310630	334297-334398	345364-345414	363824-363974	373255-373262
PDB 3AVKb, LEDGFa Site	284399-284430	310631-310865	334399-334500	345415-345465	363975-364125	373263-373270
PDB 3AVKb, LEDGFb Site	284431-284462	310866-311100	334501-334602	345466-345516	364126-364276	373271-373278
PDB 3AVKb, Y3a Site	284463-284494	311101-311335	334603-334704	345517-345567	364277-364427	373279-373286
PDB 3AVKb, Y3b Site	284495-284526	311336-311570	334705-334806	345568-345618	364428-364578	373287-373294
PDB 3AVLa, FBPa Site	284527-284558	311571-311805	334807-334908	345619-345669	364579-364729	373295-373302
PDB 3AVLa, FBPb Site	284559-284590	311806-312040	334909-335010	345670-345720	364730-364880	373303-373310
PDB 3AVLa, LEDGFa Site	284591-284622	312041-312275	335011-335112	345721-345771	364881-365031	373311-373318
PDB 3AVLa, LEDGFb Site	284623-284654	312276-312510	335113-335214	345772-345822	365032-365182	373319-373326
PDB 3AVLa, Y3a Site	284655-284686	312511-312745	335215-335316	345823-345873	365183-365333	373327-373334
PDB 3AVLa, Y3b Site	284687-284718	312746-312980	335317-335418	345874-345924	365334-365484	373335-373342
PDB 3AVLb, FBPa Site	284719-284750	312981-313215	335419-335520	345925-345975	365485-365635	373343-373350
PDB 3AVLb, FBPb Site	284751-284782	313216-313450	335521-335622	345976-346026	365636-365786	373351-373358
PDB 3AVLb, LEDGFa Site	284783-284814	313451-313685	335623-335724	346027-346077	365787-365937	373359-373366
PDB 3AVLb, LEDGFb Site	284815-284846	313686-313920	335725-335826	346078-346128	365938-366088	373367-373374
PDB 3AVLb, Y3a Site	284847-284878	313921-314155	335827-335928	346129-346179	366089-366239	373375-373382
PDB 3AVLb, Y3b Site	284879-284910	314156-314390	335929-336030	346180-346230	366240-366390	373383-373390
PDB 3AVMa, FBPa Site	284911-284942	314391-314625	336031-336132	346231-346281	366391-366541	373391-373398
PDB 3AVMa, FBPb Site	284943-284974	314626-314860	336133-336234	346282-346332	366542-366692	373399-373406
PDB 3AVMa, LEDGFa Site	284975-285006	314861-315095	336235-336336	346333-346383	366693-366843	373407-373414
PDB 3AVMa, LEDGFb Site	285007-285038	315096-315330	336337-336438	346384-346434	366844-366994	373415-373422
PDB 3AVMa, Y3a Site	285039-285070	315331-315565	336439-336540	346435-346485	366995-367145	373423-373430
PDB 3AVMa, Y3b Site	285071-285102	315566-315800	336541-336642	346486-346536	367146-367296	373431-373438
PDB 3AVMb, FBPa Site	285103-285134	315801-316035	336643-336744	346537-346587	367297-367447	373439-373446
PDB 3AVMb, FBPb Site	285135-285166	316036-316270	336745-336846	346588-346638	367448-367598	373447-373454
PDB 3AVMb, LEDGFa Site	285167-285198	316271-316505	336847-336948	346639-346689	367599-367749	373455-373462
PDB 3AVMb, LEDGFb Site	285199-285230	316506-316740	336949-337050	346690-346740	367750-367900	373463-373470
PDB 3AVMb, Y3a Site	285231-285262	316741-316975	337051-337152	346741-346791	367901-368051	373471-373478
PDB 3AVMb, Y3b Site	285263-285294	316976-317210	337153-337254	346792-346842	368052-368202	373479-373486
PDB 3AVNa, FBPa Site	285295-285326	317211-317445	337255-337356	346843-346893	368203-368353	373487-373494
PDB 3AVNa, FBPb Site	285327-285358	317446-317680	337357-337458	346894-346944	368354-368504	373495-373502
PDB 3AVNa, LEDGFa Site	285359-285390	317681-317915	337459-337560	346945-346995	368505-368655	373503-373510
PDB 3AVNa, LEDGFb Site	285391-285422	317916-318150	337561-337662	346996-347046	368656-368806	373511-373518
PDB 3AVNa, Y3a Site	285423-285454	318151-318385	337663-337764	347047-347097	368807-368957	373519-373526
PDB 3AVNa, Y3b Site	285455-285486	318386-318620	337765-337866	347098-347148	368958-369108	373527-373534
PDB 3AVNb, FBPa Site	285487-285518	318621-318855	337867-337968	347149-347199	369109-369259	373535-373542
PDB 3AVNb, FBPb Site	285519-285550	318856-319090	337969-338070	347200-347250	369260-369410	373543-373550
PDB 3AVNb, LEDGFa Site	285551-285582	319091-319325	338071-338172	347251-347301	369411-369561	373551-373558
PDB 3AVNb, LEDGFb Site	285583-285614	319326-319560	338173-338274	347302-347352	369562-369712	373559-373566
PDB 3AVNb, Y3a Site	285615-285646	319561-319795	338275-338376	347353-347403	369713-369863	373567-373574
PDB 3AVNb, Y3b Site	285647-285678	319796-320030	338377-338478	347404-347454	369864-370014	373575-373582
PDB 4GVMa, FBPa Site	285679-285710	320031-320265	338479-338580	347455-347505	370015-370165	373583-373590
PDB 4GVMa, FBPb Site	285711-285742	320266-320500	338581-338682	347506-347556	370166-370316	373591-373598
PDB 4GVMa, LEDGFa Site	285743-285774	320501-320735	338683-338784	347557-347607	370317-370467	373599-373606
PDB 4GVMa, LEDGFb Site	285775-285806	320736-320970	338785-338886	347608-347658	370468-370618	373607-373614
PDB 4GVMb, FBPa Site	285807-285838	320971-321205	338887-338988	347659-347709	370619-370769	373615-373622
PDB 4GVMb, FBPb Site	285839-285870	321206-321440	338989-339090	347710-347760	370770-370920	373623-373630
PDB 4GVMb, LEDGFa Site	285871-285902	321441-321675	339091-339192	347761-347811	370921-371071	373631-373638
PDB 4GVMb, LEDGFb Site	285903-285934	321676-321910	339193-339294	347812-347862	371072-371222	373639-373646
PDB 4GW6a, FBPa Site	285935-285966	321911-322145	339295-339396	347863-347913	371223-371373	373647-373654
PDB 4GW6a, FBPb Site	285967-285998	322146-322380	339397-339498	347914-347964	371374-371524	373655-373662
PDB 4GW6a, LEDGFa Site	285999-286030	322381-322615	339499-339600	347965-348015	371525-371675	373663-373670
PDB 4GW6a, LEDGFb Site	286031-286062	322616-322850	339601-339702	348016-348066	371676-371826	373671-373678
PDB 4GW6b, FBPa Site	286063-286094	322851-323085	339703-339804	348067-348117	371827-371977	373679-373686
PDB 4GW6b, FBPb Site	286095-286126	323086-323320	339805-339906	348118-348168	371978-372128	373687-373694
PDB 4GW6b, LEDGFa Site	286127-286158	323321-323555	339907-340008	348169-348219	372129-372279	373695-373702
PDB 4GW6b, LEDGFb Site	286159-286190	323556-323790	340009-340110	348220-348270	372280-372430	373703-373710
COMPLETION	9.8%	0.6%	0%	0%	0%	0%

Experiments 97 to 102 (AD Vina), 0% completed

Experiments 97 through 102 target allosteric sites of HIV integrase (FBP, LEDGF, and Y3 (under the 140s residues loop) sites) using the flexible residue feature in AutoDock Vina. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge with AD Vina against various structures from the PDB. These experiments complement Experiments 47 - 51, 91 - 96; and the resulting data will help discriminate receptor structures when many are available for a virtual screening as well as evaluate flexible docking with AutoDock Vina.

*TARGET: FBP, LEDGF, and ,Y3 Sites of HIV Integrase*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 97 AD Vina Exp. 49	AD Exp. 98 AD Vina Exp. 50	AD Exp. 99 AD Vina Exp. 51	AD Exp. 100 AD Vina Exp. 52	AD Exp. 101 AD Vina Exp. 53	AD Exp. 102 AD Vina Exp. 54
PDB 3AO1, FBPa Site	197695-197726	202303-202537	236143-236244	250831-250881	258175-258325	279919-279926
PDB 3AO1, FBPb Site	197727-197758	202538-202772	236245-236346	250882-250932	258326-258476	279927-279934
PDB 3AO1, LEDGFa Site	197759-197790	202773-203007	236347-236448	250933-250983	258477-258627	279935-279942
PDB 3AO1, LEDGFb Site	197791-197822	203008-203242	236449-236550	250984-251034	258628-258778	279943-279950
PDB 3AO2, FBPa Site	197823-197854	203243-203477	236551-236652	251035-251085	258779-258929	279951-279958
PDB 3AO2, FBPb Site	197855-197886	203478-203712	236653-236754	251086-251136	258930-259080	279959-279966
PDB 3AO2, LEDGFa Site	197887-197918	203713-203947	236755-236856	251137-251187	259081-259231	279967-279974
PDB 3AO2, LEDGFb Site	197919-197950	203948-204182	236857-236958	251188-251238	259232-259382	279975-279982
PDB 3NF6, FBPa Site	197951-197982	204183-204417	236959-237060	251239-251289	259383-259533	279983-279990
PDB 3NF6, FBPb Site	197983-198014	204418-204652	237061-237162	251290-251340	259534-259684	279991-279998
PDB 3NF6, LEDGFa Site	198015-198046	204653-204887	237163-237264	251341-251391	259685-259835	279999-280006
PDB 3NF6, LEDGFb Site	198047-198078	204888-205122	237265-237366	251392-251442	259836-259986	280007-280014
PDB 3NF6, Y3a Site	198079-198110	205123-205357	237367-237468	251443-251493	259987-260137	280015-280022
PDB 3NF6, Y3b Site	198111-198142	205358-205592	237469-237570	251494-251544	260138-260288	280023-280030
PDB 3NF6, FBPa Site	198143-198174	205593-205827	237571-237672	251545-251595	260289-260439	280031-280038
PDB 3NF6, FBPb Site	198175-198206	205828-206062	237673-237774	251596-251646	260440-260590	280039-280046
PDB 3NF6, LEDGFa Site	198207-198238	206063-206297	237775-237876	251647-251697	260591-260741	280047-280054
PDB 3NF6, LEDGFb Site	198239-198270	206298-206532	237877-237978	251698-251748	260742-260892	280055-280062
PDB 3NF6, Y3a Site	198271-198302	206533-206767	237979-238080	251749-251799	260893-261043	280063-280070
PDB 3NF6, Y3b Site	198303-198334	206768-207002	238081-238182	251800-251850	261044-261194	280071-280078
PDB 3NF7, FBPa Site	198335-198366	207003-207237	238183-238284	251851-251901	261195-261345	280079-280086
PDB 3NF7, FBPb Site	198367-198398	207238-207472	238285-238386	251902-251952	261346-261496	280087-280094
PDB 3NF7, LEDGFa Site	198399-198430	207473-207707	238387-238488	251953-252003	261497-261647	280095-280102
PDB 3NF7, LEDGFb Site	198431-198462	207708-207942	238489-238590	252004-252054	261648-261798	280103-280110
PDB 3NF7, Y3a Site	198463-198494	207943-208177	238591-238692	252055-252105	261799-261949	280111-280118
PDB 3NF7, Y3b Site	198495-198526	208178-208412	238693-238794	252106-252156	261950-262100	280119-280126
PDB 3NF7, FBPa Site	198527-198558	208413-208647	238795-238896	252157-252207	262101-262251	280127-280134
PDB 3NF7, FBPb Site	198559-198590	208648-208882	238897-238998	252208-252258	262252-262402	280135-280142
PDB 3NF7, LEDGFa Site	198591-198622	208883-209117	238999-239100	252259-252309	262403-262553	280143-280150
PDB 3NF7, LEDGFb Site	198623-198654	209118-209352	239101-239202	252310-252360	262554-262704	280151-280158
PDB 3NF7, Y3a Site	198655-198686	209353-209587	239203-239304	252361-252411	262705-262855	280159-280166
PDB 3NF7, Y3b Site	198687-198718	209588-209822	239305-239406	252412-252462	262856-263006	280167-280174
PDB 3NF8, FBPa Site	198719-198750	209823-210057	239407-239508	252463-252513	263007-263157	280175-280182
PDB 3NF8, FBPb Site	198751-198782	210058-210292	239509-239610	252514-252564	263158-263308	280183-280190
PDB 3NF8, LEDGFa Site	198783-198814	210293-210527	239611-239712	252565-252615	263309-263459	280191-280198
PDB 3NF8, LEDGFb Site	198815-198846	210528-210762	239713-239814	252616-252666	263460-263610	280199-280206
PDB 3NF8, Y3a Site	198847-198878	210763-210997	239815-239916	252667-252717	263611-263761	280207-280214
PDB 3NF8, Y3b Site	198879-198910	210998-211232	239917-240018	252718-252768	263762-263912	280215-280222
PDB 3NF8, FBPa Site	198911-198942	211233-211467	240019-240120	252769-252819	263913-264063	280223-280230
PDB 3NF8, FBPb Site	198943-198974	211468-211702	240121-240222	252820-252870	264064-264214	280231-280238
PDB 3NF8, LEDGFa Site	198975-199006	211703-211937	240223-240324	252871-252921	264215-264365	280239-280246
PDB 3NF8, LEDGFb Site	199007-199038	211938-212172	240325-240426	252922-252972	264366-264516	280247-280254
PDB 3NF8, Y3a Site	199039-199070	212173-212407	240427-240528	252973-253023	264517-264667	280255-280262
PDB 3NF8, Y3b Site	199071-199102	212408-212642	240529-240630	253024-253074	264668-264818	280263-280270
PDB 3NF9, FBPa Site	199103-199134	212643-212877	240631-240732	253075-253125	264819-264969	280271-280278
PDB 3NF9, FBPb Site	199135-199166	212878-213112	240733-240834	253126-253176	264970-265120	280279-280286
PDB 3NF9, LEDGFa Site	199167-199198	213113-213347	240835-240936	253177-253227	265121-265271	280287-280294
PDB 3NF9, LEDGFb Site	199199-199230	213348-213582	240937-241038	253228-253278	265272-265422	280295-280302
PDB 3NF9, Y3a Site	199231-199262	213583-213817	241039-241140	253279-253329	265423-265573	280303-280310
PDB 3NF9, Y3b Site	199263-199294	213818-214052	241141-241242	253330-253380	265574-265724	280311-280318
PDB 3NF9, FBPa Site	199295-199326	214053-214287	241243-241344	253381-253431	265725-265875	280319-280326
PDB 3NF9, FBPb Site	199327-199358	214288-214522	241345-241446	253432-253482	265876-266026	280327-280334
PDB 3NF9, LEDGFa Site	199359-199390	214523-214757	241447-241548	253483-253533	266027-266177	280335-280342
PDB 3NF9, LEDGFb Site	199391-199422	214758-214992	241549-241650	253534-253584	266178-266328	280343-280350
PDB 3NF9, Y3a Site	199423-199454	214993-215227	241651-241752	253585-253635	266329-266479	280351-280358
PDB 3NF9, Y3b Site	199455-199486	215228-215462	241753-241854	253636-253686	266480-266630	280359-280366
PDB 3NFA, FBPa Site	199487-199518	215463-215697	241855-241956	253687-253737	266631-266781	280367-280374
PDB 3NFA, FBPb Site	199519-199550	215698-215932	241957-242058	253738-253788	266782-266932	280375-280382
PDB 3NFA, LEDGFa Site	199551-199582	215933-216167	242059-242160	253789-253839	266933-267083	280383-280390
PDB 3NFA, LEDGFb Site	199583-199614	216168-216402	242161-242262	253840-253890	267084-267234	280391-280398
PDB 3NFA, Y3a Site	199615-199646	216403-216637	242263-242364	253891-253941	267235-267385	280399-280406
PDB 3NFA, Y3b Site	199647-199678	216638-216872	242365-242466	253942-253992	267386-267536	280407-280414
PDB 3NFA, FBPa Site	199679-199710	216873-217107	242467-242568	253993-254043	267537-267687	280415-280422
PDB 3NFA, FBPb Site	199711-199742	217108-217342	242569-242670	254044-254094	267688-267838	280423-280430
PDB 3NFA, LEDGFa Site	199743-199774	217343-217577	242671-242772	254095-254145	267839-267989	280431-280438
PDB 3NFA, LEDGFb Site	199775-199806	217578-217812	242773-242874	254146-254196	267990-268140	280439-280446
PDB 3NFA, Y3a Site	199807-199838	217813-218047	242875-242976	254197-254247	268141-268291	280447-280454
PDB 3NFA, Y3b Site	199839-199870	218048-218282	242977-243078	254248-254298	268292-268442	280455-280462
PDB 3VQ4, FBPa Site	199871-199902	218283-218517	243079-243180	254299-254349	268443-268593	280463-280470
PDB 3VQ4, FBPb Site	199903-199934	218518-218752	243181-243282	254350-254400	268594-268744	280471-280478
PDB 3VQ4, LEDGFa Site	199935-199966	218753-218987	243283-243384	254401-254451	268745-268895	280479-280486
PDB 3VQ4, LEDGFb Site	199967-199998	218988-219222	243385-243486	254452-254502	268896-269046	280487-280494
PDB 3VQ5, FBPa Site	199999-200030	219223-219457	243487-243588	254503-254553	269047-269197	280495-280502
PDB 3VQ5, FBPb Site	200031-200062	219458-219692	243589-243690	254554-254604	269198-269348	280503-280510
PDB 3VQ5, LEDGFa Site	200063-200094	219693-219927	243691-243792	254605-254655	269349-269499	280511-280518
PDB 3VQ5, LEDGFb Site	200095-200126	219928-220162	243793-243894	254656-254706	269500-269650	280519-280526
PDB 3VQ7, FBPa Site	200127-200158	220163-220397	243895-243996	254707-254757	269651-269801	280527-280534
PDB 3VQ7, FBPb Site	200159-200190	220398-220632	243997-244098	254758-254808	269802-269952	280535-280542
PDB 3VQ7, LEDGFa Site	200191-200222	220633-220867	244099-244200	254809-254859	269953-270103	280543-280550
PDB 3VQ7, LEDGFb Site	200223-200254	220868-221102	244201-244302	254860-254910	270104-270254	280551-280558
PDB 3VQ8, FBPa Site	200255-200286	221103-221337	244303-244404	254911-254961	270255-270405	280559-280566
PDB 3VQ8, FBPb Site	200287-200318	221338-221572	244405-244506	254962-255012	270406-270556	280567-280574
PDB 3VQ8, LEDGFa Site	200319-200350	221573-221807	244507-244608	255013-255063	270557-270707	280575-280582
PDB 3VQ8, LEDGFb Site	200351-200382	221808-222042	244609-244710	255064-255114	270708-270858	280583-280590
PDB 3VQA, FBPa Site	200383-200414	222043-222277	244711-244812	255115-255165	270859-271009	280591-280598
PDB 3VQA, FBPb Site	200415-200446	222278-222512	244813-244914	255166-255216	271010-271160	280599-280606
PDB 3VQA, LEDGFa Site	200447-200478	222513-222747	244915-245016	255217-255267	271161-271311	280607-280614
PDB 3VQA, LEDGFb Site	200479-200510	222748-222982	245017-245118	255268-255318	271312-271462	280615-280622
PDB 3VQD, FBPa Site	200511-200542	222983-223217	245119-245220	255319-255369	271463-271613	280623-280630
PDB 3VQD, FBPb Site	200543-200574	223218-223452	245221-245322	255370-255420	271614-271764	280631-280638
PDB 3VQD, LEDGFa Site	200575-200606	223453-223687	245323-245424	255421-255471	271765-271915	280639-280646
PDB 3VQD, LEDGFb Site	200607-200638	223688-223922	245425-245526	255472-255522	271916-272066	280647-280654
PDB 3VQE, FBPa Site	200639-200670	223923-224157	245527-245628	255523-255573	272067-272217	280655-280662
PDB 3VQE, FBPb Site	200671-200702	224158-224392	245629-245730	255574-255624	272218-272368	280663-280670
PDB 3VQE, LEDGFa Site	200703-200734	224393-224627	245731-245832	255625-255675	272369-272519	280671-280678
PDB 3VQE, LEDGFb Site	200735-200766	224628-224862	245833-245934	255676-255726	272520-272670	280679-280686
PDB 3ZCM, FBPa Site	200767-200798	224863-225097	245935-246036	255727-255777	272671-272821	280687-280694
PDB 3ZCM, FBPb Site	200799-200830	225098-225332	246037-246138	255778-255828	272822-272972	280695-280702
PDB 3ZCM, LEDGFa Site	200831-200862	225333-225567	246139-246240	255829-255879	272973-273123	280703-280710
PDB 3ZCM, LEDGFb Site	200863-200894	225568-225802	246241-246342	255880-255930	273124-273274	280711-280718
PDB 3ZCM, Y3a Site	200895-200926	225803-226037	246343-246444	255931-255981	273275-273425	280719-280726
PDB 3ZCM, Y3b Site	200927-200958	226038-226272	246445-246546	255982-256032	273426-273576	280727-280734
PDB 3ZSO, FBPa Site	200959-200990	226273-226507	246547-246648	256033-256083	273577-273727	280735-280742
PDB 3ZSO, FBPb Site	200991-201022	226508-226742	246649-246750	256084-256134	273728-273878	280743-280750
PDB 3ZSO, LEDGFa Site	201023-201054	226743-226977	246751-246852	256135-256185	273879-274029	280751-280758
PDB 3ZSO, LEDGFb Site	201055-201086	226978-227212	246853-246954	256186-256236	274030-274180	280759-280766
PDB 3ZSO, Y3a Site	201087-201118	227213-227447	246955-247056	256237-256287	274181-274331	280767-280774
PDB 3ZSO, Y3b Site	201119-201150	227448-227682	247057-247158	256288-256338	274332-274482	280775-280782
PDB 3ZSW, FBPa Site	201151-201182	227683-227917	247159-247260	256339-256389	274483-274633	280783-280790
PDB 3ZSW, FBPb Site	201183-201214	227918-228152	247261-247362	256390-256440	274634-274784	280791-280798
PDB 3ZSW, LEDGFa Site	201215-201246	228153-228387	247363-247464	256441-256491	274785-274935	280799-280806
PDB 3ZSW, LEDGFb Site	201247-201278	228388-228622	247465-247566	256492-256542	274936-275086	280807-280814
PDB 3ZSW, Y3a Site	201279-201310	228623-228857	247567-247668	256543-256593	275087-275237	280815-280822
PDB 3ZSW, Y3b Site	201311-201342	228858-229092	247669-247770	256594-256644	275238-275388	280823-280830
PDB 3ZT1, FBPa Site	201343-201374	229093-229327	247771-247872	256645-256695	275389-275539	280831-280838
PDB 3ZT1, FBPb Site	201375-201406	229328-229562	247873-247974	256696-256746	275540-275690	280839-280846
PDB 3ZT1, LEDGFa Site	201407-201438	229563-229797	247975-248076	256747-256797	275691-275841	280847-280854
PDB 3ZT1, LEDGFb Site	201439-201470	229798-230032	248077-248178	256798-256848	275842-275992	280855-280862
PDB 3ZT1, Y3a Site	201471-201502	230033-230267	248179-248280	256849-256899	275993-276143	280863-280870
PDB 3ZT1, Y3b Site	201503-201534	230268-230502	248281-248382	256900-256950	276144-276294	280871-280878
PDB 3ZT2, FBPa Site	201535-201566	230503-230737	248383-248484	256951-257001	276295-276445	280879-280886
PDB 3ZT2, FBPb Site	201567-201598	230738-230972	248485-248586	257002-257052	276446-276596	280887-280894
PDB 3ZT2, LEDGFa Site	201599-201630	230973-231207	248587-248688	257053-257103	276597-276747	280895-280902
PDB 3ZT2, LEDGFb Site	201631-201662	231208-231442	248689-248790	257104-257154	276748-276898	280903-280910
PDB 3ZT2, Y3a Site	201663-201694	231443-231677	248791-248892	257155-257205	276899-277049	280911-280918
PDB 3ZT2, Y3b Site	201695-201726	231678-231912	248893-248994	257206-257256	277050-277200	280919-280926
PDB 3ZT3, FBPa Site	201727-201758	231913-232147	248995-249096	257257-257307	277201-277351	280927-280934
PDB 3ZT3, FBPb Site	201759-201790	232148-232382	249097-249198	257308-257358	277352-277502	280935-280942
PDB 3ZT3, LEDGFa Site	201791-201822	232383-232617	249199-249300	257359-257409	277503-277653	280943-280950
PDB 3ZT3, LEDGFb Site	201823-201854	232618-232852	249301-249402	257410-257460	277654-277804	280951-280958
PDB 3ZT3, Y3a Site	201855-201886	232853-233087	249403-249504	257461-257511	277805-277955	280959-280966
PDB 3ZT3, Y3b Site	201887-201918	233088-233322	249505-249606	257512-257562	277956-278106	280967-280974
PDB 3ZT4, FBPa Site	201919-201950	233323-233557	249607-249708	257563-257613	278107-278257	280975-280982
PDB 3ZT4, FBPb Site	201951-201982	233558-233792	249709-249810	257614-257664	278258-278408	280983-280990
PDB 3ZT4, LEDGFa Site	201983-202014	233793-234027	249811-249912	257665-257715	278409-278559	280991-280998
PDB 3ZT4, LEDGFb Site	202015-202046	234028-234262	249913-250014	257716-257766	278560-278710	280999-281006
PDB 3ZT4, Y3a Site	202047-202078	234263-234497	250015-250116	257767-257817	278711-278861	281007-281014
PDB 3ZT4, Y3b Site	202079-202110	234498-234732	250117-250218	257818-257868	278862-279012	281015-281022
PDB 4AHR, FBPa Site	202111-202142	234733-234967	250219-250320	257869-257919	279013-279163	281023-281030
PDB 4AHR, FBPb Site	202143-202174	234968-235202	250321-250422	257920-257970	279164-279314	281031-281038
PDB 4AHR, LEDGFa Site	202175-202206	235203-235437	250423-250524	257971-258021	279315-279465	281039-281046
PDB 4AHR, LEDGFb Site	202207-202238	235438-235672	250525-250626	258022-258072	279466-279616	281047-281054
PDB 4AHR, Y3a Site	202239-202270	235673-235907	250627-250728	258073-258123	279617-279767	281055-281062
PDB 4AHR, Y3b Site	202271-202302	235908-236142	250729-250830	258124-258174	279768-279918	281063-281070
COMPLETION	0%	0%	0%	0%	0%	0%

Experiments 91 to 96 (AD Vina), 72% completed

Experiments 91 through 96 (AD Vina Experiments 43 to 48) target allosteric sites of HIV integrase. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge with AD Vina against various structures from the PDB. These experiments complement Experiments 47 - 51, and the resulting data will help discriminate receptor structures when many are available for a virtual screening.

*TARGET: FBP, LEDGF, and ,Y3 Sites of HIV Integrase*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 91 AD Vina Exp. 43	AD Exp. 92 AD Vina Exp. 44	AD Exp. 93 AD Vina Exp. 45	AD Exp. 94 AD Vina Exp. 46	AD Exp. 95 AD Vina Exp. 47	AD Exp. 96 AD Vina Exp. 48
PDB 3NF6_A, FBP Site	168745-168776	170345-170579	182095-182196	187195-187245	189745-189895	197295-197302
PDB 3NF6_B, FBP Site	168777-168808	170580-170814	182197-182298	187246-187296	189896-190046	197303-197310
PDB 3NF7_A, FBP Site	168809-168840	170815-171049	182299-182400	187297-187347	190047-190197	197311-197318
PDB 3NF7_B, FBP Site	168841-168872	171050-171284	182401-182502	187348-187398	190198-190348	197319-197326
PDB 3NF8_A, FBP Site	168873-168904	171285-171519	182503-182604	187399-187449	190349-190499	197327-197334
PDB 3NF9_A, FBP Site	168905-168936	171520-171754	182605-182706	187450-187500	190500-190650	197335-197342
PDB 3NF9_B, FBP Site	168937-168968	171755-171989	182707-182808	187501-187551	190651-190801	197343-197350
PDB 3NFA_A, FBP Site	168969-169000	171990-172224	182809-182910	187552-187602	190802-190952	197351-197358
PDB 3NFA_B, FBP Site	169001-169032	172225-172459	182911-183012	187603-187653	190953-191103	197359-197366
PDB 3VQ8_B, FBP Site	169033-169064	172460-172694	183013-183114	187654-187704	191104-191254	197367-197374
PDB 3ZCM_A, FBP Site	169065-169096	172695-172929	183115-183216	187705-187755	191255-191405	197375-197382
PDB 3ZSO_B, FBP Site	169097-169128	172930-173164	183217-183318	187756-187806	191406-191556	197383-197390
PDB 3ZSW_B, FBP Site	169129-169160	173165-173399	183319-183420	187807-187857	191557-191707	197391-197398
PDB 3ZT1_A, FBP Site	169161-169192	173400-173634	183421-183522	187858-187908	191708-191858	197399-197406
PDB 3ZT2_A, FBP Site	169193-169224	173635-173869	183523-183624	187909-187959	191859-192009	197407-197414
PDB 3ZT3_A, FBP Site	169225-169256	173870-174104	183625-183726	187960-188010	192010-192160	197415-197422
PDB 3ZT4_B, FBP Site	169257-169288	174105-174339	183727-183828	188011-188061	192161-192311	197423-197430
PDB 3AO1, LEDGF Site	169289-169320	174340-174574	183829-183930	188062-188112	192312-192462	197431-197438
PDB 3AO2, LEDGF Site	169321-169352	174575-174809	183931-184032	188113-188163	192463-192613	197439-197446
PDB 3NF6_B, LEDGF Site	169353-169384	174810-175044	184033-184134	188164-188214	192614-192764	197447-197454
PDB 3NF7_A, LEDGF Site	169385-169416	175045-175279	184135-184236	188215-188265	192765-192915	197455-197462
PDB 3NF7_B, LEDGF Site	169417-169448	175280-175514	184237-184338	188266-188316	192916-193066	197463-197470
PDB 3NF8_B, LEDGF Site	169449-169480	175515-175749	184339-184440	188317-188367	193067-193217	197471-197478
PDB 3NF9_A, LEDGF Site	169481-169512	175750-175984	184441-184542	188368-188418	193218-193368	197479-197486
PDB 3NF9_B, LEDGF Site	169513-169544	175985-176219	184543-184644	188419-188469	193369-193519	197487-197494
PDB 3NFA_A, LEDGF Site	169545-169576	176220-176454	184645-184746	188470-188520	193520-193670	197495-197502
PDB 3NFA_B, LEDGF Site	169577-169608	176455-176689	184747-184848	188521-188571	193671-193821	197503-197510
PDB 3VQ4, LEDGF Site	169609-169640	176690-176924	184849-184950	188572-188622	193822-193972	197511-197518
PDB 3VQ5_A, LEDGF Site	169641-169672	176925-177159	184951-185052	188623-188673	193973-194123	197519-197526
PDB 3VQ7, LEDGF Site	169673-169704	177160-177394	185053-185154	188674-188724	194124-194274	197527-197534
PDB 3VQA, LEDGF Site	169705-169736	177395-177629	185155-185256	188725-188775	194275-194425	197535-197542
PDB 3VQD, LEDGF Site	169737-169768	177630-177864	185257-185358	188776-188826	194426-194576	197543-197550
PDB 3VQE_A, LEDGF Site	169769-169800	177865-178099	185359-185460	188827-188877	194577-194727	197551-197558
PDB 4AHR_A, LEDGF Site	169801-169832	178100-178334	185461-185562	188878-188928	194728-194878	197559-197566
PDB 3AO1, Y3 Site	169833-169864	178335-178569	185563-185664	188929-188979	194879-195029	197567-197574
PDB 3AO2, Y3 Site	169865-169896	178570-178804	185665-185766	188980-189030	195030-195180	197575-197582
PDB 3VQ4, Y3 Site	169897-169928	178805-179039	185767-185868	189031-189081	195181-195331	197583-197590
PDB 3VQ5_A, Y3 Site	169929-169960	179040-179274	185869-185970	189082-189132	195332-195482	197591-197598
PDB 3VQ8_B, Y3 Site	169961-169992	179275-179509	185971-186072	189133-189183	195483-195633	197599-197606
PDB 3VQA, Y3 Site	169993-170024	179510-179744	186073-186174	189184-189234	195634-195784	197607-197614
PDB 3VQD, Y3 SiteA	170025-170056	179745-179979	186175-186276	189235-189285	195785-195935	197615-197622
PDB 3VQE_A, Y3 Site	170057-170088	179980-180214	186277-186378	189286-189336	195936-196086	197623-197630
PDB 3ZCM_A, Y3 Site	170089-170120	180215-180449	186379-186480	189337-189387	196087-196237	197631-197638
PDB 3ZSO_B, Y3 Site	170121-170152	180450-180684	186481-186582	189388-189438	196238-196388	197639-197646
PDB 3ZSW_B, Y3 Site	170153-170184	180685-180919	186583-186684	189439-189489	196389-196539	197647-197654
PDB 3ZT1_A, Y3 Site	170185-170216	180920-181154	186685-186786	189490-189540	196540-196690	197655-197662
PDB 3ZT2_A, Y3 Site	170217-170248	181155-181389	186787-186888	189541-189591	196691-196841	197663-197670
PDB 3ZT3_A, Y3 Site	170249-170280	181390-181624	186889-186990	189592-189642	196842-196992	197671-197678
PDB 3ZT4_B, Y3 Site	170281-170312	181625-181859	186991-187092	189643-189693	196993-197143	197679-197686
PDB 4AHR_A, Y3 Site	170313-170344	181860-182094	187093-187194	189694-189744	197144-197294	197687-197694
COMPLETION	99.9%	99.1%	97.2%	88.2%	46.4%	0%

Experiments 85 to 90 (AD Vina), 83% completed

Experiments 85 through 90 (AD Vina Experiments 37 to 42) target allosteric sites of HIV protease. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge with AD Vina against various structures from the PDB.

Receptor Information (Total of 72)

PDB Codes of Included Structures 1ZTZ 3IW8 3KF0 3KFN 3KFP 3KFR 3KFS 3T11 4DQG 4E43
Allosteric Sites of Chain A (and B for all but 3I8W and KFP) 1F1 Disulfide Exo Ear

*TARGET: 4 Allosteric Sites of HIV-1 Protease (PR)*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 85	AD Exp. 86	AD Exp. 87	AD Exp. 88	AD Exp. 89	AD Exp. 90
PDB 1ZTZ, 1F1 Site, Chain A	127057-127088	129361-129595	146281-146382	153625-153675	157297-157447	168169-168176
PDB 1ZTZ, 1F1 Site, Chain B	127089-127120	129596-129830	146383-146484	153676-153726	157448-157598	168177-168184
PDB 1ZTZ, Disulfide Site, Chain A	127121-127152	129831-130065	146485-146586	153727-153777	157599-157749	168185-168192
PDB 1ZTZ, Disulfide Site, Chain B	127153-127184	130066-130300	146587-146688	153778-153828	157750-157900	168193-168200
PDB 1ZTZ, "Ear" Site, Chain A	127185-127216	130301-130535	146689-146790	153829-153879	157901-158051	168201-168208
PDB 1ZTZ, "Ear" Site, Chain B	127217-127248	130536-130770	146791-146892	153880-153930	158052-158202	168209-168216
PDB 1ZTZ, 4d9 and DMSO Sites, Chain A	127249-127280	130771-131005	146893-146994	153931-153981	158203-158353	168217-168224
PDB 1ZTZ, 4d9 and DMSO Sites, Chain B	127281-127312	131006-131240	146995-147096	153982-154032	158354-158504	168225-168232
PDB 3I8W Monomer, 1F1 Site	127313-127344	131241-131475	147097-147198	154033-154083	158505-158655	168233-168240
PDB 3I8W Monomer, Disulfide Site	127345-127376	131476-131710	147199-147300	154084-154134	158656-158806	168241-168248
PDB 3I8W Monomer, "Ear" Site	127377-127408	131711-131945	147301-147402	154135-154185	158807-158957	168249-168256
PDB 3I8W Monomer, 4d9 and DMSO Sites	127409-127440	131946-132180	147403-147504	154186-154236	158958-159108	168257-168264
PDB 3KF0, 1F1 Site, Chain A	127441-127472	132181-132415	147505-147606	154237-154287	159109-159259	168265-168272
PDB 3KF0, 1F1 Site, Chain B	127473-127504	132416-132650	147607-147708	154288-154338	159260-159410	168273-168280
PDB 3KF0, Disulfide Site, Chain A	127505-127536	132651-132885	147709-147810	154339-154389	159411-159561	168281-168288
PDB 3KF0, Disulfide Site, Chain B	127537-127568	132886-133120	147811-147912	154390-154440	159562-159712	168289-168296
PDB 3KF0, "Ear" Site, Chain A	127569-127600	133121-133355	147913-148014	154441-154491	159713-159863	168297-168304
PDB 3KF0, "Ear" Site, Chain B	127601-127632	133356-133590	148015-148116	154492-154542	159864-160014	168305-168312
PDB 3KF0, 4d9 and DMSO Sites, Chain A	127633-127664	133591-133825	148117-148218	154543-154593	160015-160165	168313-168320
PDB 3KF0, 4d9 and DMSO Sites, Chain B	127665-127696	133826-134060	148219-148320	154594-154644	160166-160316	168321-168328
PDB 3KFN, 1F1 Site, Chain A	127697-127728	134061-134295	148321-148422	154645-154695	160317-160467	168329-168336
PDB 3KFN, 1F1 Site, Chain B	127729-127760	134296-134530	148423-148524	154696-154746	160468-160618	168337-168344
PDB 3KFN, Disulfide Site, Chain A	127761-127792	134531-134765	148525-148626	154747-154797	160619-160769	168345-168352
PDB 3KFN, Disulfide Site, Chain B	127793-127824	134766-135000	148627-148728	154798-154848	160770-160920	168353-168360
PDB 3KFN, "Ear" Site, Chain A	127825-127856	135001-135235	148729-148830	154849-154899	160921-161071	168361-168368
PDB 3KFN, "Ear" Site, Chain B	127857-127888	135236-135470	148831-148932	154900-154950	161072-161222	168369-168376
PDB 3KFN, 4d9 and DMSO Sites, Chain A	127889-127920	135471-135705	148933-149034	154951-155001	161223-161373	168377-168384
PDB 3KFN, 4d9 and DMSO Sites, Chain B	127921-127952	135706-135940	149035-149136	155002-155052	161374-161524	168385-168392
PDB 3KFP Monomer, 1F1 Site	127953-127984	135941-136175	149137-149238	155053-155103	161525-161675	168393-168400
PDB 3KFP Monomer, Disulfide Site	127985-128016	136176-136410	149239-149340	155104-155154	161676-161826	168401-168408
PDB 3KFP Monomer, "Ear" Site	128017-128048	136411-136645	149341-149442	155155-155205	161827-161977	168409-168416
PDB 3KFP Monomer, 4d9 and DMSO Sites	128049-128080	136646-136880	149443-149544	155206-155256	161978-162128	168417-168424
PDB 3KFR, 1F1 Site, Chain A	128081-128112	136881-137115	149545-149646	155257-155307	162129-162279	168425-168432
PDB 3KFR, 1F1 Site, Chain B	128113-128144	137116-137350	149647-149748	155308-155358	162280-162430	168433-168440
PDB 3KFR, Disulfide Site, Chain A	128145-128176	137351-137585	149749-149850	155359-155409	162431-162581	168441-168448
PDB 3KFR, Disulfide Site, Chain B	128177-128208	137586-137820	149851-149952	155410-155460	162582-162732	168449-168456
PDB 3KFR, "Ear" Site, Chain A	128209-128240	137821-138055	149953-150054	155461-155511	162733-162883	168457-168464
PDB 3KFR, "Ear" Site, Chain B	128241-128272	138056-138290	150055-150156	155512-155562	162884-163034	168465-168472
PDB 3KFR, 4d9 and DMSO Sites, Chain A	128273-128304	138291-138525	150157-150258	155563-155613	163035-163185	168473-168480
PDB 3KFR, 4d9 and DMSO Sites, Chain B	128305-128336	138526-138760	150259-150360	155614-155664	163186-163336	168481-168488
PDB 3KFS, 1F1 Site, Chain A	128337-128368	138761-138995	150361-150462	155665-155715	163337-163487	168489-168496
PDB 3KFS, 1F1 Site, Chain B	128369-128400	138996-139230	150463-150564	155716-155766	163488-163638	168497-168504
PDB 3KFS, Disulfide Site, Chain A	128401-128432	139231-139465	150565-150666	155767-155817	163639-163789	168505-168512
PDB 3KFS, Disulfide Site, Chain B	128433-128464	139466-139700	150667-150768	155818-155868	163790-163940	168513-168520
PDB 3KFS, "Ear" Site, Chain A	128465-128496	139701-139935	150769-150870	155869-155919	163941-164091	168521-168528
PDB 3KFS, "Ear" Site, Chain B	128497-128528	139936-140170	150871-150972	155920-155970	164092-164242	168529-168536
PDB 3KFS, 4d9 and DMSO Sites, Chain A	128529-128560	140171-140405	150973-151074	155971-156021	164243-164393	168537-168544
PDB 3KFS, 4d9 and DMSO Sites, Chain B	128561-128592	140406-140640	151075-151176	156022-156072	164394-164544	168545-168552
PDB 3T11, 1F1 Site, Chain A	128593-128624	140641-140875	151177-151278	156073-156123	164545-164695	168553-168560
PDB 3T11, 1F1 Site, Chain B	128625-128656	140876-141110	151279-151380	156124-156174	164696-164846	168561-168568
PDB 3T11, Disulfide Site, Chain A	128657-128688	141111-141345	151381-151482	156175-156225	164847-164997	168569-168576
PDB 3T11, Disulfide Site, Chain B	128689-128720	141346-141580	151483-151584	156226-156276	164998-165148	168577-168584
PDB 3T11, "Ear" Site, Chain A	128721-128752	141581-141815	151585-151686	156277-156327	165149-165299	168585-168592
PDB 3T11, "Ear" Site, Chain B	128753-128784	141816-142050	151687-151788	156328-156378	165300-165450	168593-168600
PDB 3T11, 4d9 and DMSO Sites, Chain A	128785-128816	142051-142285	151789-151890	156379-156429	165451-165601	168601-168608
PDB 3T11, 4d9 and DMSO Sites, Chain B	128817-128848	142286-142520	151891-151992	156430-156480	165602-165752	168609-168616
PDB 4DQG, 1F1 Site, Chain A	128849-128880	142521-142755	151993-152094	156481-156531	165753-165903	168617-168624
PDB 4DQG, 1F1 Site, Chain B	128881-128912	142756-142990	152095-152196	156532-156582	165904-166054	168625-168632
PDB 4DQG, Disulfide Site, Chain A	128913-128944	142991-143225	152197-152298	156583-156633	166055-166205	168633-168640
PDB 4DQG, Disulfide Site, Chain B	128945-128976	143226-143460	152299-152400	156634-156684	166206-166356	168641-168648
PDB 4DQG, "Ear" Site, Chain A	128977-129008	143461-143695	152401-152502	156685-156735	166357-166507	168649-168656
PDB 4DQG, "Ear" Site, Chain B	129009-129040	143696-143930	152503-152604	156736-156786	166508-166658	168657-168664
PDB 4DQG, 4d9 and DMSO Sites, Chain A	129041-129072	143931-144165	152605-152706	156787-156837	166659-166809	168665-168672
PDB 4DQG, 4d9 and DMSO Sites, Chain B	129073-129104	144166-144400	152707-152808	156838-156888	166810-166960	168673-168680
PDB 4E43, 1F1 Site, Chain A	129105-129136	144401-144635	152809-152910	156889-156939	166961-167111	168681-168688
PDB 4E43, 1F1 Site, Chain B	129137-129168	144636-144870	152911-153012	156940-156990	167112-167262	168689-168696
PDB 4E43, Disulfide Site, Chain A	129169-129200	144871-145105	153013-153114	156991-157041	167263-167413	168697-168704
PDB 4E43, Disulfide Site, Chain B	129201-129232	145106-145340	153115-153216	157042-157092	167414-167564	168705-168712
PDB 4E43, "Ear" Site, Chain A	129233-129264	145341-145575	153217-153318	157093-157143	167565-167715	168713-168720
PDB 4E43, "Ear" Site, Chain B	129265-129296	145576-145810	153319-153420	157144-157194	167716-167866	168721-168728
PDB 4E43, 4d9 and DMSO Sites, Chain A	129297-129328	145811-146045	153421-153522	157195-157245	167867-168017	168729-168736
PDB 4E43, 4d9 and DMSO Sites, Chain B	129329-129360	146046-146280	153523-153624	157246-157296	168018-168168	168737-168744
COMPLETION	100%	99.9%	99.9%	0%	99.9%	99.8%

Experiments 79 to 84 (AD Vina), 95% completed

Experiments 79 through 84 target (AD Vina Experiments 31 to 36) the exo site region of HIV protease; they are the same experiments as Experiments 73 - 78, but Vina is used instead of AutoDock. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge with AD Vina against a crystal structure from the Stout Lab and PDB 3KF0.

*TARGET: Exo Site Region of HIV-1 Protease (PR)*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 79 (31)	AD Exp. 80 (32)	AD Exp. 81 (33)	AD Exp. 82 (34)	AD Exp. 83 (35)	AD Exp. 84 (36)
PDB, 3KF0, Chain A	124401-124432	124529-124763	125469-125570	125877-125927	126081-126231	126685-126692
Stout Lab Structure, Chain A	124433-124464	124764-124998	125571-125672	125928-125978	126232-126382	126693-126700
PDB, 3KF0, Chain B	124465-124496	124999-125233	125673-125774	125979-126029	126383-126533	126701-126708
Stout Lab Structure, Chain B	124497-124528	125234-125468	125775-125876	126030-126080	126534-126684	126709-126716
COMPLETION	100%	100%	100%	100%	100%	100%

Experiments 73 to 78 (AutoDock), 17% completed

Experiments 73 through 78 target the exo site region of HIV protease. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M) and Maybridge with AutoDock against a crystal structure from the Stout Lab and PDB 3KF0.

*TARGET: Exo Site Region of HIV-1 Protease (PR)*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M	Maybridge
	AD Exp. 73	AD Exp. 74	AD Exp. 75	AD Exp. 76	AD Exp. 77	AD Exp. 78
PDB, 3KF0, Chain A	101653-101969	102921-105265	112301-113314	116357-116863	118385-119888	124401-124477
Stout Lab Structure, Chain A	101970-102286	105266-107610	113315-114328	116864-117370	119889-121392	124478-124554
PDB, 3KF0, Chain B	102287-102603	107611-109955	114329-115342	117371-117877	121393-122896	124555-124631
Stout Lab Structure, Chain B	102604-102920	109956-112300	115343-116356	117878-118384	122897-124400	124632-124708
COMPLETION	99.2%	3.7%	0%	0%	0%	0%

Experiment 72 (AutoDock), 99.8% Complete

Experiments 72 targets the 4d9 site of HIV-1 protease (PR). This experiment involves screening the full NCI Set against 2 crystal structures and focuses on refining future AutoDock (and AD Vina) virtual screenings. These dockings will be compared with past dockings to the full NCI Set against PR to help overall efficiency in terms of accuracy and speed.

Batch summary by parameters*:

Batches 97215 - 97848: usual parameters run by Dr. Perryman (ALP)

Batches 97849 - 98482: default AutoDock parameters (GA*)

Batches 98483 - 99116: default AutoDock parameters (GA*) on fragment structures only

Batches 99117 - 99750: default AutoDock parameters

Batches 99751 - 100384: default AutoDock parameters on fragment structures only

Batches 100385 - 101018: default AutoDock parameters except elitism = 5

Batches 101019 - 101652: default AutoDock parameters except elitism = 10
*All batches in this experiment are done with new docking box parameters.

*TARGET: 4d9 Site of HIV-1 Protease (PR), Full NCI Set*
Receptor Structure	ALP Parameters	Default AD Parameters (GA)*	Default AD Parameters Fragments Only(GA*)	Default AD Parameters	Default AD Parameters Fragments Only	Elitism = 5	Elitism = 10
PDB 3KF0	97215-97531	97849-98165	98483-98799	99117-99433	99751-100067	100385-100701	101019-101335
Stout Lab C6-bound structure	97532-97848	98166-98482	98800-99116	99434-99750	100068-100384	100702-101018	101336-101652

*GA is the traditional genetic algorithm, and the Lamarckian genetic algorithm (LGA) is the current default AutoDock method.

Experiments 52 to 71 = AD Vina Exp. 11 to 30, 100% completed

Experiments 52 through 71 (AD Vina Experiments 11 to 30) target the three allosteric sites of HIV reverse transcriptase as well as the known non-nucleoside reverse trasciptase inhibitor (NNRTI) site. These experiments involve screening 5 large libraries (Full NCI, Enamine, ChemBridge, Asinex and Vitas-M) with AD Vina against several crystal structures and molecular dynamics (MD) snapshots from the McCammon Lab, UCSD. Among the crystal structures are those from our collaborators in the Arnold Lab. The MD snapshots were graciously provided by Sara Nichols, from simulations on PDB 1VRT (see the supporting information of Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening by Nichols et. al.). Positive control dockings were first performed to choose appropriate MD snapshots for each target. While performing these initial studies, different docking parameters were tested involving placement of the docking bounding box in which docking calculations are performed.

Experiment summary by site:

Exp. 52 - 56: incoming nucleotide binding site (INuB) of HIV-1 Reverse Transcriptase (RT)

Exp. 57 - 61: knuckles binding site (KNUC) of HIV-1 Reverse Transcriptase (RT)

Exp. 62 - 66: NNRTI adjacent site (NNRTIadj) of HIV-1 Reverse Trascriptase (RT)

Exp. 67 - 71: NNRTI binding site (NNRTI site) of HIV-1 Reverse Transcriptase (RT)

*TARGET: Incoming Nucleotide Binding Site (INuB) of HIV-1 Reverse Transcriptase (RT)*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M
	AD Exp. 52 Vina Exp. 11	AD Exp. 53 Vina Exp. 12	AD Exp. 54 Vina Exp. 13	AD Exp. 55 Vina Exp. 14	AD Exp. 56 Vina Exp. 15
MD snapshot uc1_frame_963	63526 - 63557	64006 - 64240	67531 - 67632	69061 - 69111	69826 - 69976
MD snapshot apa_frame_1633	63558 - 63589	64241 - 64475	67633 - 67734	69112 - 69162	69977 - 70127
MD snapshot apa_frame_1598	63590 - 63621	64476 - 64710	67735 - 67836	69163 - 69213	70128 - 70278
MD snapshot apa_frame_1693	63622 - 63653	64711 - 64945	67837 - 67938	69214 - 69264	70279 - 70429
MD snapshot apa_frame_1649	63654 - 63685	64946 - 65180	67939 - 68040	69265 - 69315	70430 - 70580
MD snapshot uc1_frame_455	63686 - 63717	65181 - 65415	68041 - 68142	69316 - 69366	70581 - 70731
MD snapshot uc1_frame_1241	63718 - 63749	65416 - 65650	68143 - 68244	69367 - 69417	70732 - 70882
MD snapshot uc1_frame_1198	63750 - 63781	65651 - 65885	68245 - 68346	69418 - 69468	70883 - 71033
PDB 1VRU, w/NNRTI*	63782 - 63813	65886 - 66120	68347 - 68448	69469 - 69519	71034 - 71184
PDB 1VRU, w/out NNRTI*	63814 - 63845	66121 - 66355	68449 - 68550	69520 - 69570	71185 - 71335
PDB 2ZD1, w/out NNRTI*	63846 - 63877	66356 - 66590	68551 - 68652	69571 - 69621	71336 - 71486
PDB 4ICL, w/out NNRTI*	63878 - 63909	66591 - 66825	68653 - 68754	69622 - 69672	71487 - 71637
PDB 4ICL, w/NNRTI*	63910 - 63941	66826 - 67060	68755 - 68856	69673 - 69723	71638 - 71788
PDB 4KFB, w/out NNRTI*	63942 - 63973	67061 - 67295	68857 - 68958	69724 - 69774	71789 - 71939
PDB 4KFB, w/NNRTI*	63974 - 64005	67296 - 67530	68959 - 69060	69775 - 69825	71940 - 72090
COMPLETION	100%	100%	100%	100%	100%

*"NNRTI" is non-nucleoside HIV reverse transcriptase inhibitor.

*TARGET: Knuckles Binding Site (KNUC) of HIV-1 Reverse Transcriptase (RT)*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M
	AD Exp. 57 AD Vina Exp. 16	AD Exp. 58 AD Vina Exp. 17	AD Exp. 59 AD Vina Exp. 18	AD Exp. 60 AD Vina Exp. 19	AD Exp. 61 AD Vina Exp. 20
MD snapshot apa_frame_1701	72091 - 72122	72411 - 72645	74761 - 74862	75781 - 75831	76291 - 76441
MD snapshot apa_frame_1702	72123 - 72154	72646 - 72880	74863 - 74964	75832 - 75882	76442 - 76592
PDB 1FK9, w/NNRTI*	72155 - 72186	72881 - 73115	74965 - 75066	75883 - 75933	76593 - 76743
PDB 1FK9, w/out NNRTI*	72187 - 72218	73116 - 73350	75067 - 75168	75934 - 75984	76744 - 76894
PDB 4IFY, w/out NNRTI* [KNUC and INuB sites centered]	72219 - 72250	73351 - 73585	75169 - 75270	75985 - 76035	76895 - 77045
PDB 4IFY, w/out NNRTI* [KNUC site centered]	72251 - 72282	73586 - 73820	75271 - 75372	76036 - 76086	77046 - 77196
PDB 4IFY, w/NNRTI* [KNUC and INuB sites centered]	72283 - 72314	73821 - 74055	75373 - 75474	76087 - 76137	77197 - 77347
PDB 4KFB, w/out NNRTI* [KNUC and INuB sites centered]	72315 - 72346	74056 - 74290	75475 - 75576	76138 - 76188	77348 - 77498
PDB 4KFB, w/out NNRTI* [KNUC site centered]	72347 - 72378	74291 - 74525	75577 - 75678	76189 - 76239	77499 - 77649
PDB 4KFB, w/NNRTI* [KNUC and INuB sites centered]	72379 - 72410	74526 - 74760	75679 - 75780	76240 - 76290	77650 - 77800
COMPLETION	100%	100%	100%	100%	100%

*"NNRTI" is non-nucleoside HIV reverse transcriptase inhibitor.

*TARGET: NNRTI Adjacent Site (NNRTIadj) of HIV-1 Reverse Transcriptase (RT)*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M
	AD Exp. 62 AD Vina Exp. 21	AD Exp. 63 AD Vina Exp. 22	AD Exp. 64 AD Vina Exp. 23	AD Exp. 65 AD Vina Exp. 24	AD Exp. 66 AD Vina Exp. 25
PDB 2ZD1, w/NNRTI*	77801 - 77832	77897 - 78131	78602 - 78703	78908 - 78958	79061 - 79211
PDB 4IFY, w/NNRTI*	77833 - 77864	78132 - 78366	78704 - 78805	78959 - 79009	79212 - 79362
PDB 4KFB, w/NNRTI*	77865 - 77896	78367 - 78601	78806 - 78907	79010 - 79060	79363 - 79513
COMPLETION	100%	100%	100%	100%	100%

*"NNRTI" is non-nucleoside HIV reverse transcriptase inhibitor.

*TARGET: NNRTI Site of HIV-1 Reverse Transcriptase (RT)*
Receptor Structure	Full NCI	Enamine	ChemBridge	Asinex	Vitas-M
	AD Exp. 67 AD Vina Exp. 26	AD Exp. 68 AD Vina Exp. 27	AD Exp. 69 AD Vina Exp. 28	AD Exp. 70 AD Vina Exp. 29	AD Exp. 71 AD Vina Exp. 30
MD snapshot uc1_frame_963	79514 - 79545	80506 - 80740	87791 - 87892	90953 - 91003	92534 - 92684
MD snapshot uc1_frame_209	79546 - 79577	80741 - 80975	87893 - 87994	91004 - 91054	92685 - 92835
MD snapshot uc1_frame_1452	79578 - 79609	80976 - 81210	87995 - 88096	91055 - 91105	92836 - 92986
MD snapshot apa_frame_1701	79610 - 79641	81211 - 81445	88097 - 88198	91106 - 91156	92987 - 93137
MD snapshot uc1_frame_1781	79642 - 79673	81446 - 81680	88199 - 88300	91157 - 91207	93138 - 93288
MD snapshot uc1_frame_326	79674 - 79705	81681 - 81915	88301 - 88402	91208 - 91258	93289 - 93439
MD snapshot uc1_frame_63	79706 - 79737	81916 - 82150	88403 - 88504	91259 - 91309	93440 - 93590
MD snapshot uc1_frame_693	79738 - 79769	82151 - 82385	88505 - 88606	91310 - 91360	93591 - 93741
MD snapshot uc1_frame_1076	79770 - 79801	82386 - 82620	88607 - 88708	91361 - 91411	93742 - 93892
MD snapshot uc1_frame_978	79802 - 79833	82621 - 82855	88709 - 88810	91412 - 91462	93893 - 94043
MD snapshot uc1_frame_1038	79834 - 79865	82856 - 83090	88811 - 88912	91463 - 91513	94044 - 94194
MD snapshot apa_frame_1301	79866 - 79897	83091 - 83325	88913 - 89014	91514 - 91564	94195 - 94345
MD snapshot uc1_frame_205	79898 - 79929	83326 - 83560	89015 - 89116	91565 - 91615	94346 - 94496
MD snapshot apa_frame_1845	79930 - 79961	83561 - 83795	89117 - 89218	91616 - 91666	94497 - 94647
MD snapshot uc1_frame_1062	79962 - 79993	83796 - 84030	89219 - 89320	91667 - 91717	94648 - 94798
MD snapshot uc1_frame_455	79994 - 80025	84031 - 84265	89321 - 89422	91718 - 91768	94799 - 94949
MD snapshot uc1_frame_128	80026 - 80057	84266 - 84500	89423 - 89524	91769 - 91819	94950 - 95100
MD snapshot uc1_frame_572	80058 - 80089	84501 - 84735	89525 - 89626	91820 - 91870	95101 - 95251
MD snapshot uc1_frame_653	80090 - 80121	84736 - 84970	89627 - 89728	91871 - 91921	95252 - 95402
MD snapshot apa_frame_1628	80122 - 80153	84971 - 85205	89729 - 89830	91922 - 91972	95403 - 95553
MD snapshot uc1_frame_1198	80154 - 80185	85206 - 85440	89831 - 89932	91973 - 92023	95554 - 95704
PDB 1BQM	80186 - 80217	85441 - 85675	89933 - 90034	92024 - 92074	95705 - 95855
PDB 1EP4	80218 - 80249	85676 - 85910	90035 - 90136	92075 - 92125	95856 - 96006
PDB 1FK9	80250 - 80281	85911 - 86145	90137 - 90238	92126 - 92176	96007 - 96157
PDB 1KLM	80282 - 80313	86146 - 86380	90239 - 90340	92177 - 92227	96158 - 96308
PDB 1RT1	80314 - 80345	86381 - 86615	90341 - 90442	92228 - 92278	96309 - 96459
PDB 1RT4	80346 - 80377	86616 - 86850	90443 - 90544	92279 - 92329	96460 - 96610
PDB 1VRT	80378 - 80409	86851 - 87085	90545 - 90646	92330 - 92380	96611 - 96761
PDB 1VRU	80410 - 80441	87086 - 87320	90647 - 90748	92381 - 92431	96762 - 96912
PDB 2ZD1	80442 - 80473	87321 - 87555	90749 - 90850	92432 - 92482	96913 - 97063
PDB 4IFY	80474 - 80505	87556 - 87790	90851 - 90952	92483 - 92533	97064 - 97214
COMPLETION	99.7%	99.9%	99.9%	100%	100%

Experiments 47 to 51 = AD Vina Exp. 6 to 10, 99% completed

Experiments 47 through 51 (that is, AD Vina Experiments 6 to 10) target the three recently-discovered allosteric sites of HIV integrase. These experiments involve screening ~ 5.6 million compounds against 30 models of different crystal structures of HIV integrase (or "IN"). Each of these crystal structures (3-D, atomically-detailed maps of the location of all of the atoms of the protein) involved an allosteric inhibitor bound to at least one of these three allosteric sites (but some of these allosteric inhibitors were fragments that bound to two or three of these different allosteric sites simultaneously). Thus, we are screening compounds against allosteric-inhibitor-induced conformations (or shapes) of HIV integrase.

HIV integrase is one of the three viral enzymes that must work properly in order for HIV to replicate itself and spread. Specifically, HIV integrase processes and then permanently attaches (or "integrates") the viral cDNA into the human genomic DNA of the cells that HIV infects.

To learn what "allosteric inhibitors are," see page 4 of Volume 11 of our FightAIDS@Home Newsletter.

In these 5 experiments with AD Vina (see http://vina.scripps.edu), we will be trying to discover new compounds that can bind to at least one of the three allosteric sites of HIV integrase, which are called the "LEDGF site," the "FBP" (for Fragment Binding Pocket), or the "Y3 site" (which is adjacent to the region underneath the "140s loop"). To learn more about these allosteric sites on the catalytic core domain of HIV integrase, see this paper by the Deadman group, this paper by the Scanlon group, this newer paper by the Scanlon group, or see this paper by Alan Engelman, Jacques J. Kessl, and Mamuka Kvaratskhelia.

The Engelman and Kvaratskhelia labs, and several other labs at 6 different institutions around the country, recently started collaborating with the Olson lab, as part of the new NIH-funded Center called the "HIVE." Click on this link to a press release about the creation of the HIVE, or click on the logo above to explore the http://HIVE.scripps.edu website.

Experiment 47 = AD Vina Exp. 6 = 100% completed
[NCI library = 316,179 models of compounds]
46396 - 46427 = NCI library versus the FBP allosteric site of IN from 3AO1.pdb
46428 - 46459 = NCI library versus the FBP allosteric site of IN from 3AO2.pdb
46460 - 46491 = NCI library versus the FBP allosteric site of IN from 3NF8_B.pdb
46492 - 46523 = NCI library versus the FBP allosteric site of IN from 3VQ4.pdb
46524 - 46555 = NCI library versus the FBP allosteric site of IN from 3VQ5_A.pdb
46556 - 46587 = NCI library versus the FBP allosteric site of IN from 3VQ7.pdb
46588 - 46619 = NCI library versus the FBP allosteric site of IN from 3VQA.pdb
46620 - 46651 = NCI library versus the FBP allosteric site of IN from 3VQD.pdb
46652 - 46683 = NCI library versus the FBP allosteric site of IN from 3VQE_A.pdb
46684 - 46715 = NCI library versus the FBP allosteric site of IN from 4AHR_A.pdb
46716 - 46747 = NCI library versus the LEDGF allosteric site of IN from 3NF6_A.pdb
46748 - 46779 = NCI library versus the LEDGF allosteric site of IN from 3NF8_A.pdb
46780 - 46811 = NCI library versus the LEDGF allosteric site of IN from 3VQ8_B.pdb
46812 - 46843 = NCI library versus the LEDGF allosteric site of IN from 3ZCM_A.pdb
46844 - 46875 = NCI library versus the LEDGF allosteric site of IN from 3ZSO_B.pdb
46876 - 46907 = NCI library versus the LEDGF allosteric site of IN from 3ZSW_B.pdb
46908 - 46939 = NCI library versus the LEDGF allosteric site of IN from 3ZT1_A.pdb
46940 - 46971 = NCI library versus the LEDGF allosteric site of IN from 3ZT2_A.pdb
46972 - 47003 = NCI library versus the LEDGF allosteric site of IN from 3ZT3_A.pdb
47004 - 47035 = NCI library versus the LEDGF allosteric site of IN from 3ZT4_B.pdb
47036 - 47067 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_A.pdb
47068 - 47099 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_B.pdb
47100 - 47131 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_A.pdb
47132 - 47163 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_B.pdb
47164 - 47195 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_A.pdb
47196 - 47227 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_B.pdb
47228 - 47259 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_A.pdb
47260 - 47291 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_B.pdb
47292 - 47323 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_A.pdb
47324 - 47355 = NCI library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_B.pdb

Experiment 48 = AD Vina Exp. 7 = 99.9% completed
[Enamine library = 2,345,014 models of compounds]
47356 - 47590 = Enamine library versus the FBP allosteric site of IN from 3AO1.pdb
47591 - 47825 = Enamine library versus the FBP allosteric site of IN from 3AO2.pdb
47826 - 48060 = Enamine library versus the FBP allosteric site of IN from 3NF8_B.pdb
48061 - 48295 = Enamine library versus the FBP allosteric site of IN from 3VQ4.pdb
48296 - 48530 = Enamine library versus the FBP allosteric site of IN from 3VQ5_A.pdb
48531 - 48765 = Enamine library versus the FBP allosteric site of IN from 3VQ7.pdb
48766 - 49000 = Enamine library versus the FBP allosteric site of IN from 3VQA.pdb
49001 - 49235 = Enamine library versus the FBP allosteric site of IN from 3VQD.pdb
49236 - 49470 = Enamine library versus the FBP allosteric site of IN from 3VQE_A.pdb
49471 - 49705 = Enamine library versus the FBP allosteric site of IN from 4AHR_A.pdb
49706 - 49940 = Enamine library versus the LEDGF allosteric site of IN from 3NF6_A.pdb
49941 - 50175 = Enamine library versus the LEDGF allosteric site of IN from 3NF8_A.pdb
50176 - 50410 = Enamine library versus the LEDGF allosteric site of IN from 3VQ8_B.pdb
50411 - 50645 = Enamine library versus the LEDGF allosteric site of IN from 3ZCM_A.pdb
50646 - 50880 = Enamine library versus the LEDGF allosteric site of IN from 3ZSO_B.pdb
50881 - 51115 = Enamine library versus the LEDGF allosteric site of IN from 3ZSW_B.pdb
51116 - 51350 = Enamine library versus the LEDGF allosteric site of IN from 3ZT1_A.pdb
51351 - 51585 = Enamine library versus the LEDGF allosteric site of IN from 3ZT2_A.pdb
51586 - 51820 = Enamine library versus the LEDGF allosteric site of IN from 3ZT3_A.pdb
51821 - 52055 = Enamine library versus the LEDGF allosteric site of IN from 3ZT4_B.pdb
52056 - 52290 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_A.pdb
52291 - 52525 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_B.pdb
52526 - 52760 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_A.pdb
52761 - 52995 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_B.pdb
52996 - 53230 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_A.pdb
53231 - 53465 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_B.pdb
53466 - 53700 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_A.pdb
53701 - 53935 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_B.pdb
53936 - 54170 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_A.pdb
54171 - 54405 = Enamine library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_B.pdb

Experiment 49 = AD Vina Exp. 8 = 100% completed
[ChemBridge library = 1,013,483 models of compounds]
54406 - 54507 = ChemBridge library versus the FBP allosteric site of IN from 3AO1.pdb
54508 - 54609 = ChemBridge library versus the FBP allosteric site of IN from 3AO2.pdb
54610 - 54711 = ChemBridge library versus the FBP allosteric site of IN from 3NF8_B.pdb
54712 - 54813 = ChemBridge library versus the FBP allosteric site of IN from 3VQ4.pdb
54814 - 54915 = ChemBridge library versus the FBP allosteric site of IN from 3VQ5_A.pdb
54916 - 55017 = ChemBridge library versus the FBP allosteric site of IN from 3VQ7.pdb
55018 - 55119 = ChemBridge library versus the FBP allosteric site of IN from 3VQA.pdb
55120 - 55221 = ChemBridge library versus the FBP allosteric site of IN from 3VQD.pdb
55222 - 55323 = ChemBridge library versus the FBP allosteric site of IN from 3VQE_A.pdb
55324 - 55425 = ChemBridge library versus the FBP allosteric site of IN from 4AHR_A.pdb
55426 - 55527 = ChemBridge library versus the LEDGF allosteric site of IN from 3NF6_A.pdb
55528 - 55629 = ChemBridge library versus the LEDGF allosteric site of IN from 3NF8_A.pdb
55630 - 55731 = ChemBridge library versus the LEDGF allosteric site of IN from 3VQ8_B.pdb
55732 - 55833 = ChemBridge library versus the LEDGF allosteric site of IN from 3ZCM_A.pdb
55834 - 55935 = ChemBridge library versus the LEDGF allosteric site of IN from 3ZSO_B.pdb
55936 - 56037 = ChemBridge library versus the LEDGF allosteric site of IN from 3ZSW_B.pdb
56038 - 56139 = ChemBridge library versus the LEDGF allosteric site of IN from 3ZT1_A.pdb
56140 - 56241 = ChemBridge library versus the LEDGF allosteric site of IN from 3ZT2_A.pdb
56242 - 56343 = ChemBridge library versus the LEDGF allosteric site of IN from 3ZT3_A.pdb
56344 - 56445 = ChemBridge library versus the LEDGF allosteric site of IN from 3ZT4_B.pdb
56446 - 56547 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_A.pdb
56548 - 56649 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_B.pdb
56650 - 56751 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_A.pdb
56752 - 56853 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_B.pdb
56854 - 56955 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_A.pdb
56956 - 57057 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_B.pdb
57058 - 57159 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_A.pdb
57160 - 57261 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_B.pdb
57262 - 57363 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_A.pdb
57364 - 57465 = ChemBridge library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_B.pdb

Experiment 50 = AD Vina Exp. 9 = 100% completed
[Asinex library = 507,000 models of compounds]
57466 - 57516 = Asinex library versus the FBP allosteric site of IN from 3AO1.pdb
57517 - 57567 = Asinex library versus the FBP allosteric site of IN from 3AO2.pdb
57568 - 57618 = Asinex library versus the FBP allosteric site of IN from 3NF8_B.pdb
57619 - 57669 = Asinex library versus the FBP allosteric site of IN from 3VQ4.pdb
57670 - 57720 = Asinex library versus the FBP allosteric site of IN from 3VQ5_A.pdb
57721 - 57771 = Asinex library versus the FBP allosteric site of IN from 3VQ7.pdb
57772 - 57822 = Asinex library versus the FBP allosteric site of IN from 3VQA.pdb
57823 - 57873 = Asinex library versus the FBP allosteric site of IN from 3VQD.pdb
57874 - 57924 = Asinex library versus the FBP allosteric site of IN from 3VQE_A.pdb
57925 - 57975 = Asinex library versus the FBP allosteric site of IN from 4AHR_A.pdb
57976 - 58026 = Asinex library versus the LEDGF allosteric site of IN from 3NF6_A.pdb
58027 - 58077 = Asinex library versus the LEDGF allosteric site of IN from 3NF8_A.pdb
58078 - 58128 = Asinex library versus the LEDGF allosteric site of IN from 3VQ8_B.pdb
58129 - 58179 = Asinex library versus the LEDGF allosteric site of IN from 3ZCM_A.pdb
58180 - 58230 = Asinex library versus the LEDGF allosteric site of IN from 3ZSO_B.pdb
58231 - 58281 = Asinex library versus the LEDGF allosteric site of IN from 3ZSW_B.pdb
58282 - 58332 = Asinex library versus the LEDGF allosteric site of IN from 3ZT1_A.pdb
58333 - 58383 = Asinex library versus the LEDGF allosteric site of IN from 3ZT2_A.pdb
58384 - 58434 = Asinex library versus the LEDGF allosteric site of IN from 3ZT3_A.pdb
58435 - 58485 = Asinex library versus the LEDGF allosteric site of IN from 3ZT4_B.pdb
58486 - 58536 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_A.pdb
58537 - 58587 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_B.pdb
58588 - 58638 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_A.pdb
58639 - 58689 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_B.pdb
58690 - 58740 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_A.pdb
58741 - 58791 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_B.pdb
58792 - 58842 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_A.pdb
58843 - 58893 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_B.pdb
58894 - 58944 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_A.pdb
58945 - 58995 = Asinex library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_B.pdb

Experiment 51 = AD Vina Exp. 10 = 100% completed
[Vitas-M Labs library = 1,503,273 models of compounds]
58996 - 59146 = Vitas-M Labs library versus the FBP allosteric site of IN from 3AO1.pdb
59147 - 59297 = Vitas-M Labs library versus the FBP allosteric site of IN from 3AO2.pdb
59298 - 59448 = Vitas-M Labs library versus the FBP allosteric site of IN from 3NF8_B.pdb
59449 - 59599 = Vitas-M Labs library versus the FBP allosteric site of IN from 3VQ4.pdb
59600 - 59750 = Vitas-M Labs library versus the FBP allosteric site of IN from 3VQ5_A.pdb
59751 - 59901 = Vitas-M Labs library versus the FBP allosteric site of IN from 3VQ7.pdb
59902 - 60052 = Vitas-M Labs library versus the FBP allosteric site of IN from 3VQA.pdb
60053 - 60203 = Vitas-M Labs library versus the FBP allosteric site of IN from 3VQD.pdb
60204 - 60354 = Vitas-M Labs library versus the FBP allosteric site of IN from 3VQE_A.pdb
60355 - 60505 = Vitas-M Labs library versus the FBP allosteric site of IN from 4AHR_A.pdb
60506 - 60656 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3NF6_A.pdb
60657 - 60807 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3NF8_A.pdb
60808 - 60958 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3VQ8_B.pdb
60959 - 61109 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3ZCM_A.pdb
61110 - 61260 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3ZSO_B.pdb
61261 - 61411 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3ZSW_B.pdb
61412 - 61562 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3ZT1_A.pdb
61563 - 61713 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3ZT2_A.pdb
61714 - 61864 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3ZT3_A.pdb
61865 - 62015 = Vitas-M Labs library versus the LEDGF allosteric site of IN from 3ZT4_B.pdb
62016 - 62166 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_A.pdb
62167 - 62317 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF6_B.pdb
62318 - 62468 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_A.pdb
62469 - 62619 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF7_B.pdb
62620 - 62770 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_A.pdb
62771 - 62921 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF8_B.pdb
62922 - 63072 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_A.pdb
63073 - 63223 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NF9_B.pdb
63224 - 63374 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_A.pdb
63375 - 63525 = Vitas-M Labs library versus the Y3 allosteric site of IN (under 140s loop) from 3NFA_B.pdb

Experiments 42 to 46 = AD Vina Exp. 1 to 5, 100% completed

Experiments 42 through 46 (that is, AD Vina Experiments 1 to 5) involve screening ~ 5.6 million compounds against two models of a recently-discovered allosteric site of HIV reverse transcriptase. Reverse transcriptase (or "RT") is one of the three viral enzymes that must work properly in order for HIV to replicate itself and spread. These are the first FightAIDS@Home experiments that target the RT system.

To learn what "allosteric inhibitors are," see page 4 of Volume 11 of our FightAIDS@Home Newsletter.

In these first 5 experiments with AD Vina (see http://vina.scripps.edu), we will be trying to discover new compounds that can bind to the "NNRTI adjacent" allosteric site of RT. This NNRTI adjacent allosteric site, and two other recently-discovered allosteric sites on HIV reverse transcriptase, were discovered by Eddy Arnold's lab at Rutgers University. To learn about these allosteric sites, click on this link.

Eddy Arnold's lab, and several other labs at 6 different institutions around the country, recently started collaborating with the Olson lab, as part of the new NIH-funded Center called the "HIVE." Click on this link to a press release about the creation of the HIVE, or click on the logo above to explore the http://HIVE.scripps.edu website.

Experiment 42 = AD Vina Exp. 1 = 100% completed
[Enamine library = 2,345,014 models of compounds]
45254 - 45488 = Enamine vs. NNRTI adjacent site of RT in 4I7G.pdb, with NNRTI drug present in the target
45489 - 45723 = Enamine vs. NNRTI adjacent site of RT in 4I7G.pdb, without the NNRTI drug present

Experiment 43 = AD Vina Exp. 2 = 100% completed
[NCI library = 316,179 models of compounds]
45724 - 45755 = NCI vs. NNRTI adjacent site of RT in 4I7G.pdb, with NNRTI drug present in the target
45756 - 45787 = NCI vs. NNRTI adjacent site of RT in 4I7G.pdb, without the NNRTI drug present

Experiment 44 = AD Vina Exp. 3 = 100% completed
[ChemBridge library = 1,013,483 models of compounds]
45788 - 45889 = ChemBridge vs. NNRTI adjacent site of RT in 4I7G.pdb, with NNRTI drug present
45890 - 45991 = ChemBridge vs. NNRTI adjacent site of RT in 4I7G.pdb, without the NNRTI drug present

Experiment 45 = AD Vina Exp. 4 = 100% completed
[Asinex library = 507,000 models of compounds]
45992 - 46042 = Asinex vs. NNRTI adjacent site of RT in 4I7G.pdb, with NNRTI drug present in the target
46043 - 46093 = Asinex vs. NNRTI adjacent site of RT in 4I7G.pdb, without the NNRTI drug present

Experiment 46 = AD Vina Exp. 5 = 100% completed
[Vitas-M Labs library = 1,503,273 models of compounds]
46094 - 46244 = Vitas-M Labs vs. NNRTI adjacent site of RT in 4I7G.pdb, with NNRTI drug present
46245 - 46395 = Vitas-M Labs vs. NNRTI adjacent site of RT in 4I7G.pdb, without the NNRTI drug present

Experiment 41: 99% Completed

Experiment 41 involves screening the Enamine library of 2.345 million compounds against the two allosteric sites on the surface of HIV protease. Experiment 41 and all previous FAAH experiments were performed with the software "AutoDock" (see http://autodock.scripps.edu ). This experiment is similar to Exp. 36 (see page 2 of the Status for a description of Exp. 36), but a different, much larger library of compounds is being screened, and some new targets are being included. The first part of this experiment involves docking compounds against the two allosteric-fragment-bound crystal structures presented in our recent article in Chemical Biology and Drug Design, vol. 75: 257-268 (March 2010). Three other, brand new crystal structures from Dave Stout's lab that involve allosteric fragments bound to these two sites on the surface of HIV protease are also being used as targets. Two of these new targets are presented in a new research manuscript from the Stout lab that is currently being peer-reviewed. When this paper is accepted, we will describe these targets in more detail and provide a link to this new paper.

This is by far the largest experiment we have submitted to FightAIDS@Home; it involves faah33,529 - faah45,253.

The results of these calculations started arriving at TSRI on 5/15/2012.

Experiment 40: 100% Completed

Experiment 40 involves screening the ChemBridge library of 1,013,483 models of compounds against the newly-discovered allosteric binding site on HIV-1 integrase. This new allosteric binding site (which we are also targeting in Experiments 38 and 39) was discovered by Professor John J. Deadman's group, and it was described in "Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design," by D.I. Rhodes, T.S. Peat, J.J. Deadman, et al., published in the journal Antiviral Chemistry and Chemotherapy, 21: 155-168 (2011). The new crystal structure from this paper that contains the atomically-detailed, 3-D data on this new allosteric site is called "3NF6.pdb". We are screening compounds against this allosteric site to try to discover new, larger, more potent allosteric inhibitors of HIV-1 integrase. It is hoped that these new allosteric inhibitors of integrase will be effective at disabling the current drug-resistant mutant superbugs of HIV integrase. For more information about this new allosteric site, see Volume 10 of the FightAIDS@Home newsletter or our recent World AIDS Day webinar (both are linked at the top of the homepage for this site).

Similar to Experiment 39, in Experiment 40 we are screening one million compounds against the new allosteric site on HIV-1 integrase using two slightly different docking approaches: in the first half of these calculations, we are using the smaller dimensions of the "grid box" (the region that the compounds are allowed to explore during the docking calculations) that produced the best results in the "positive control" docking calculations that reproduced the known binding mode of this new allosteric fragment (see the figures in Volume 10 of the FAAH Newsletter, page 8). In the second half of these calculations, we are using a larger grid box, to try to find even larger allosteric inhibitors that can bind strongly with both the allosteric site and other sub-pockets that are adjacent to it.

This experiment involves faah31,501 - faah33,528.

These results began arriving at TSRI on 3/24/2012, and the experiment finished 5/29/2012.

Experiment 39: 100% Completed

Experiment 39 involves screening the Enamine library of 2,345,014 compounds against the newly-discovered allosteric binding site on HIV-1 integrase. This new allosteric binding site (which we are also targeting in Experiment 38) was discovered by Professor John J. Deadman's group, and it was described in "Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design," by D.I. Rhodes, T.S. Peat, J.J. Deadman, et al., published in the journal Antiviral Chemistry and Chemotherapy, 21: 155-168 (2011). The new crystal structure from this paper that contains the atomically-detailed, 3-D data on this new allosteric site is called "3NF6.pdb". We are screening compounds against this allosteric site to try to discover new, larger, more potent allosteric inhibitors of HIV-1 integrase. It is hoped that these new allosteric inhibitors of integrase will be effective at disabling the current drug-resistant mutant superbugs of HIV integrase. For more information about this new allosteric site, see Volume 10 of the FightAIDS@Home newsletter or our recent World AIDS Day webinar (both are linked at the top of the homepage for this site).

In Experiment 39, we are screening these 2.3 million compounds against the new allosteric site on HIV-1 integrase using two slightly different docking approaches: in the first half of these calculations, we are using the smaller dimensions of the "grid box" (the region that the compounds are allowed to explore during the docking calculations) that produced the best results in the "positive control" docking calculations that reproduced the known binding mode of this new allosteric fragment (see the figures in Volume 10 of the FAAH Newsletter, page 8). In the second half of these calculations, we are using a larger grid box, to try to find even larger allosteric inhibitors that can bind strongly with both the allosteric site and other sub-pockets that are adjacent to it.

This experiment involves faah26,811 - faah31,500.

These calculations began (that is, the results started arriving at TSRI) on 12/17/2011. The last batch of results arrived 5/15/2012.

Descriptions of the previous FightAIDS@Home experiments and of their status are available by clicking on this link.

Results of these FightAIDS@Home experiments are available to the public as raw, unprocessed AutoDock dlg files upon request. E-mail Dr. Daniel N. Santiago = dsantiag ]~[ scripps . edu (use the @ symbol to replace the ]~[ and remove the spaces) for further information. Please include the phrase "FAAH data" in the subject line of your e-mail. Since the amount of data is on the order of many terabytes, you will need to provide suitable media (such as external hard drives) for receiving a copy of these results.


Image above of an ensemble of target conformations of the G140S/Q148H drug-resistant mutant of HIV integrase was created by Alex Perryman. Created by Dr. Garrett M. Morris and curated by Dr. Alex L. Perryman from 2007 to August, 2013. Now curated by Dr. Daniel N. Santiago. The HIVE logo above was created by Dr. Stefano Forli. Last modified: 12/05/2013 by Daniel N. Santiago, Ph.D. ©2003-2013 The Olson Laboratory, The Scripps Research Institute, All Rights Reserved.