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Items: 1 to 20 of 192

1.

Statistical potential for modeling and ranking of protein-ligand interactions.

Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A.

J Chem Inf Model. 2011 Dec 27;51(12):3078-92. doi: 10.1021/ci200377u. Epub 2011 Nov 21.

3.

Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.

Greenidge PA, Kramer C, Mozziconacci JC, Sherman W.

J Chem Inf Model. 2014 Oct 27;54(10):2697-717. doi: 10.1021/ci5003735. Epub 2014 Sep 30.

PMID:
25266271
4.

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes.

Zhang C, Liu S, Zhu Q, Zhou Y.

J Med Chem. 2005 Apr 7;48(7):2325-35.

PMID:
15801826
5.

Comparative assessment of scoring functions on a diverse test set.

Cheng T, Li X, Li Y, Liu Z, Wang R.

J Chem Inf Model. 2009 Apr;49(4):1079-93. doi: 10.1021/ci9000053.

PMID:
19358517
6.

Assessing scoring functions for protein-ligand interactions.

Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd.

J Med Chem. 2004 Jun 3;47(12):3032-47.

PMID:
15163185
7.

The consequences of scoring docked ligand conformations using free energy correlations.

Spyrakis F, Amadasi A, Fornabaio M, Abraham DJ, Mozzarelli A, Kellogg GE, Cozzini P.

Eur J Med Chem. 2007 Jul;42(7):921-33. Epub 2007 Jan 21.

PMID:
17346861
8.

Scoring confidence index: statistical evaluation of ligand binding mode predictions.

Zavodszky MI, Stumpff-Kane AW, Lee DJ, Feig M.

J Comput Aided Mol Des. 2009 May;23(5):289-99. doi: 10.1007/s10822-008-9258-8. Epub 2009 Jan 20.

9.

An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.

Wang R, Lu Y, Fang X, Wang S.

J Chem Inf Comput Sci. 2004 Nov-Dec;44(6):2114-25.

PMID:
15554682
10.

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
11.

The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement.

Brylinski M, Lee SY, Zhou H, Skolnick J.

J Struct Biol. 2011 Mar;173(3):558-69. doi: 10.1016/j.jsb.2010.09.009. Epub 2010 Sep 17.

12.

Target-specific native/decoy pose classifier improves the accuracy of ligand ranking in the CSAR 2013 benchmark.

Fourches D, Politi R, Tropsha A.

J Chem Inf Model. 2015 Jan 26;55(1):63-71. doi: 10.1021/ci500519w. Epub 2014 Dec 18.

PMID:
25521713
13.

Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results.

Li Y, Han L, Liu Z, Wang R.

J Chem Inf Model. 2014 Jun 23;54(6):1717-36. doi: 10.1021/ci500081m. Epub 2014 Jun 2.

PMID:
24708446
14.

A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction.

Cheng T, Liu Z, Wang R.

BMC Bioinformatics. 2010 Apr 17;11:193. doi: 10.1186/1471-2105-11-193.

15.

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. Epub 2013 Nov 11.

PMID:
24171431
16.
17.

Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?

Korb O, Ten Brink T, Victor Paul Raj FR, Keil M, Exner TE.

J Comput Aided Mol Des. 2012 Feb;26(2):185-97. doi: 10.1007/s10822-011-9539-5. Epub 2012 Jan 10.

PMID:
22231069
18.

Comparative evaluation of 11 scoring functions for molecular docking.

Wang R, Lu Y, Wang S.

J Med Chem. 2003 Jun 5;46(12):2287-303.

PMID:
12773034
19.

An iterative knowledge-based scoring function for protein-protein recognition.

Huang SY, Zou X.

Proteins. 2008 Aug;72(2):557-79. doi: 10.1002/prot.21949.

PMID:
18247354
20.

General and targeted statistical potentials for protein-ligand interactions.

Mooij WT, Verdonk ML.

Proteins. 2005 Nov 1;61(2):272-87.

PMID:
16106379
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