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Items: 1 to 20 of 52

1.

A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain.

Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E.

J Biol Chem. 2016 Nov 4;291(45):23569-23577. Epub 2016 Sep 19.

2.

Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.

Belew RK, Forli S, Goodsell DS, O'Donnell TJ, Olson AJ.

J Chem Inf Model. 2016 Aug 22;56(8):1597-607. doi: 10.1021/acs.jcim.6b00248. Epub 2016 Jul 25.

3.

Computational protein-ligand docking and virtual drug screening with the AutoDock suite.

Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ.

Nat Protoc. 2016 May;11(5):905-19. doi: 10.1038/nprot.2016.051. Epub 2016 Apr 14.

4.

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

Ravindranath PA, Forli S, Goodsell DS, Olson AJ, Sanner MF.

PLoS Comput Biol. 2015 Dec 2;11(12):e1004586. doi: 10.1371/journal.pcbi.1004586. eCollection 2015 Dec.

5.

Covalent docking using autodock: Two-point attractor and flexible side chain methods.

Bianco G, Forli S, Goodsell DS, Olson AJ.

Protein Sci. 2016 Jan;25(1):295-301. doi: 10.1002/pro.2733. Epub 2015 Jul 7.

6.

A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA.

Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ.

J Chem Inf Model. 2015 Mar 23;55(3):645-59. doi: 10.1021/ci500672v. Epub 2015 Feb 17.

7.

Small-molecule library screening by docking with PyRx.

Dallakyan S, Olson AJ.

Methods Mol Biol. 2015;1263:243-50. doi: 10.1007/978-1-4939-2269-7_19.

PMID:
25618350
8.

Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.

Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM.

J Phys Chem B. 2015 Jan 22;119(3):976-88. doi: 10.1021/jp506376z. Epub 2014 Sep 17.

9.

AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.

Santos-Martins D, Forli S, Ramos MJ, Olson AJ.

J Chem Inf Model. 2014 Aug 25;54(8):2371-9. doi: 10.1021/ci500209e. Epub 2014 Jul 18.

10.

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.

Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM.

J Comput Aided Mol Des. 2014 Apr;28(4):475-90. doi: 10.1007/s10822-014-9711-9. Epub 2014 Feb 7.

11.
12.

Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.

Tiefenbrunn T, Forli S, Happer M, Gonzalez A, Tsai Y, Soltis M, Elder JH, Olson AJ, Stout CD.

Chem Biol Drug Des. 2014 Feb;83(2):141-8. doi: 10.1111/cbdd.12227. Epub 2013 Oct 30.

13.

Small molecule regulation of protein conformation by binding in the Flap of HIV protease.

Tiefenbrunn T, Forli S, Baksh MM, Chang MW, Happer M, Lin YC, Perryman AL, Rhee JK, Torbett BE, Olson AJ, Elder JH, Finn MG, Stout CD.

ACS Chem Biol. 2013;8(6):1223-31. doi: 10.1021/cb300611p. Epub 2013 Mar 29.

14.

Automated docking with protein flexibility in the design of femtomolar "click chemistry" inhibitors of acetylcholinesterase.

Morris GM, Green LG, Radić Z, Taylor P, Sharpless KB, Olson AJ, Grynszpan F.

J Chem Inf Model. 2013 Apr 22;53(4):898-906. doi: 10.1021/ci300545a. Epub 2013 Mar 29.

15.

Protein flexibility in virtual screening: the BACE-1 case study.

Cosconati S, Marinelli L, Di Leva FS, La Pietra V, De Simone A, Mancini F, Andrisano V, Novellino E, Goodsell DS, Olson AJ.

J Chem Inf Model. 2012 Oct 22;52(10):2697-704. doi: 10.1021/ci300390h. Epub 2012 Oct 8.

16.

The effect of crebanine on memory and cognition impairment via the alpha-7 nicotinic acetylcholine receptor.

Rojsanga P, Boonyarat C, Utsintong M, Nemecz Á, Yamauchi JG, Talley TT, Olson AJ, Matsumoto K, Vajragupta O.

Life Sci. 2012 Aug 21;91(3-4):107-14. doi: 10.1016/j.lfs.2012.06.017. Epub 2012 Jun 28.

PMID:
22749860
17.

A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.

Forli S, Olson AJ.

J Med Chem. 2012 Jan 26;55(2):623-38. doi: 10.1021/jm2005145. Epub 2012 Jan 13.

18.

A dynamic model of HIV integrase inhibition and drug resistance.

Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ.

J Mol Biol. 2010 Mar 26;397(2):600-15. doi: 10.1016/j.jmb.2010.01.033. Epub 2010 Jan 22.

19.

Virtual screening against alpha-cobratoxin.

Utsintong M, Talley TT, Taylor PW, Olson AJ, Vajragupta O.

J Biomol Screen. 2009 Oct;14(9):1109-18. doi: 10.1177/1087057109344617. Epub 2009 Sep 4.

20.

Pursuing aldose reductase inhibitors through in situ cross-docking and similarity-based virtual screening.

Cosconati S, Marinelli L, La Motta C, Sartini S, Da Settimo F, Olson AJ, Novellino E.

J Med Chem. 2009 Sep 24;52(18):5578-81. doi: 10.1021/jm901045w.

PMID:
19719141

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