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Results: 1 to 20 of 169

1.

Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets.

Proctor EA, Yin S, Tropsha A, Dokholyan NV.

Biophys J. 2012 Jan 4;102(1):144-51. doi: 10.1016/j.bpj.2011.11.4008. Epub 2012 Jan 3.

PMID:
22225808
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening.

Hsieh JH, Yin S, Wang XS, Liu S, Dokholyan NV, Tropsha A.

J Chem Inf Model. 2012 Jan 23;52(1):16-28. doi: 10.1021/ci2002507. Epub 2011 Dec 14.

PMID:
22017385
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
[PubMed - indexed for MEDLINE]
4.

Scoring functions and enrichment: a case study on Hsp90.

Konstantinou-Kirtay C, Mitchell JB, Lumley JA.

BMC Bioinformatics. 2007 Jan 26;8:27.

PMID:
17257425
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations.

Wang B, Westerhoff LM, Merz KM Jr.

J Med Chem. 2007 Oct 18;50(21):5128-34. Epub 2007 Sep 15.

PMID:
17867664
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Scoring functions for prediction of protein-ligand interactions.

Wang JC, Lin JH.

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

PMID:
23016847
[PubMed - indexed for MEDLINE]
7.

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
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
22014038
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Consensus scoring for enriching near-native structures from protein-protein docking decoys.

Liang S, Meroueh SO, Wang G, Qiu C, Zhou Y.

Proteins. 2009 May 1;75(2):397-403. doi: 10.1002/prot.22252.

PMID:
18831053
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Structure-based virtual screening with supervised consensus scoring: evaluation of pose prediction and enrichment factors.

Teramoto R, Fukunishi H.

J Chem Inf Model. 2008 Apr;48(4):747-54. doi: 10.1021/ci700464x. Epub 2008 Mar 5.

PMID:
18318474
[PubMed - indexed for MEDLINE]
11.
12.

Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

Liebeschuetz JW, Cole JC, Korb O.

J Comput Aided Mol Des. 2012 Jun;26(6):737-48. doi: 10.1007/s10822-012-9551-4. Epub 2012 Feb 28.

PMID:
22371207
[PubMed - indexed for MEDLINE]
13.

Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening?

Grigoryan AV, Wang H, Cardozo TJ.

PLoS One. 2012;7(10):e46532. doi: 10.1371/journal.pone.0046532. Epub 2012 Oct 10.

PMID:
23071584
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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. Epub 2008 Jan 23.

PMID:
18211051
[PubMed - indexed for MEDLINE]
15.

Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization.

Liu J, He X, Zhang JZ.

J Chem Inf Model. 2013 Jun 24;53(6):1306-14. doi: 10.1021/ci400067c. Epub 2013 May 20.

PMID:
23651068
[PubMed - indexed for MEDLINE]
16.

Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.

Khashan R, Zheng W, Tropsha A.

Proteins. 2012 Aug;80(9):2207-17. doi: 10.1002/prot.24110. Epub 2012 Jun 7.

PMID:
22581643
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
[PubMed - indexed for MEDLINE]
18.

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.

PMID:
19153808
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Virtual fragment screening: exploration of MM-PBSA re-scoring.

Kawatkar S, Moustakas D, Miller M, Joseph-McCarthy D.

J Comput Aided Mol Des. 2012 Aug;26(8):921-34. doi: 10.1007/s10822-012-9590-x. Epub 2012 Aug 7.

PMID:
22869295
[PubMed - indexed for MEDLINE]
20.

Investigation of MM-PBSA rescoring of docking poses.

Thompson DC, Humblet C, Joseph-McCarthy D.

J Chem Inf Model. 2008 May;48(5):1081-91. doi: 10.1021/ci700470c. Epub 2008 May 9.

PMID:
18465849
[PubMed - indexed for MEDLINE]

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