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Items: 1 to 20 of 631

1.

Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening.

Zavodszky MI, Sanschagrin PC, Korde RS, Kuhn LA.

J Comput Aided Mol Des. 2002 Dec;16(12):883-902.

PMID:
12825621
2.

The use of protein-ligand interaction fingerprints in docking.

Brewerton SC.

Curr Opin Drug Discov Devel. 2008 May;11(3):356-64. Review.

PMID:
18428089
3.

Scoring ligand similarity in structure-based virtual screening.

Zavodszky MI, Rohatgi A, Van Voorst JR, Yan H, Kuhn LA.

J Mol Recognit. 2009 Jul-Aug;22(4):280-92. doi: 10.1002/jmr.942.

PMID:
19235177
4.

Guided docking approaches to structure-based design and screening.

Fradera X, Mestres J.

Curr Top Med Chem. 2004;4(7):687-700. Review.

PMID:
15032682
5.

Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints.

Renner S, Derksen S, Radestock S, Mörchen F.

J Chem Inf Model. 2008 Feb;48(2):319-32. doi: 10.1021/ci7003626.

PMID:
18211051
6.

Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site.

Virtanen SI, Pentikäinen OT.

J Chem Inf Model. 2010 Jun 28;50(6):1005-11. doi: 10.1021/ci100121c.

PMID:
20504004
8.

Development and validation of a modular, extensible docking program: DOCK 5.

Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC.

J Comput Aided Mol Des. 2006 Oct-Nov;20(10-11):601-19.

PMID:
17149653
9.

Protein-ligand docking against non-native protein conformers.

Verdonk ML, Mortenson PN, Hall RJ, Hartshorn MJ, Murray CW.

J Chem Inf Model. 2008 Nov;48(11):2214-25. doi: 10.1021/ci8002254.

PMID:
18954138
10.

Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase.

Birch L, Murray CW, Hartshorn MJ, Tickle IJ, Verdonk ML.

J Comput Aided Mol Des. 2002 Dec;16(12):855-69.

PMID:
12825619
11.

Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

Brylinski M.

J Chem Inf Model. 2013 Nov 25;53(11):3097-112. doi: 10.1021/ci400510e.

PMID:
24171431
12.

Toward the virtual screening of Cdc25A phosphatase inhibitors with the homology modeled protein structure.

Park H, Jeon YH.

J Mol Model. 2008 Sep;14(9):833-41. doi: 10.1007/s00894-008-0311-2.

PMID:
18504625
13.

Protein flexibility in ligand docking and virtual screening to protein kinases.

Cavasotto CN, Abagyan RA.

J Mol Biol. 2004 Mar 12;337(1):209-25.

PMID:
15001363
14.

A critical assessment of docking programs and scoring functions.

Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS.

J Med Chem. 2006 Oct 5;49(20):5912-31.

PMID:
17004707
15.

A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity.

Luo W, Pei J, Zhu Y.

J Mol Model. 2010 May;16(5):903-13. doi: 10.1007/s00894-009-0598-7.

PMID:
19823881
16.

Scoring functions for prediction of protein-ligand interactions.

Wang JC, Lin JH.

Curr Pharm Des. 2013;19(12):2174-82. Review.

PMID:
23016847
18.

FlexE: efficient molecular docking considering protein structure variations.

Claussen H, Buning C, Rarey M, Lengauer T.

J Mol Biol. 2001 Apr 27;308(2):377-95.

PMID:
11327774
19.

Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening.

Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG.

J Chem Inf Model. 2008 Dec;48(12):2371-85. doi: 10.1021/ci800166p.

PMID:
19007114
20.

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

Floriano WB, Vaidehi N, Zamanakos G, Goddard WA 3rd.

J Med Chem. 2004 Jan 1;47(1):56-71.

PMID:
14695820
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