Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 192

1.

Normalizing molecular docking rankings using virtually generated decoys.

Wallach I, Jaitly N, Nguyen K, Schapira M, Lilien R.

J Chem Inf Model. 2011 Aug 22;51(8):1817-30. doi: 10.1021/ci200175h. Epub 2011 Jul 13.

PMID:
21699246
2.

Large-scale similarity search profiling of ChEMBL compound data sets.

Heikamp K, Bajorath J.

J Chem Inf Model. 2011 Aug 22;51(8):1831-9. doi: 10.1021/ci200199u. Epub 2011 Jul 14.

PMID:
21728295
3.

Ligand and decoy sets for docking to G protein-coupled receptors.

Gatica EA, Cavasotto CN.

J Chem Inf Model. 2012 Jan 23;52(1):1-6. doi: 10.1021/ci200412p. Epub 2011 Dec 14.

PMID:
22168315
4.

Virtual decoy sets for molecular docking benchmarks.

Wallach I, Lilien R.

J Chem Inf Model. 2011 Feb 28;51(2):196-202. doi: 10.1021/ci100374f. Epub 2011 Jan 5.

PMID:
21207928
5.

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
6.

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
7.

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
8.

Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: predicting affinity and conformational sampling.

Bazeley PS, Prithivi S, Struble CA, Povinelli RJ, Sem DS.

J Chem Inf Model. 2006 Nov-Dec;46(6):2698-708.

PMID:
17125210
9.

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
10.
11.

Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening.

Wei D, Zheng H, Su N, Deng M, Lai L.

J Chem Inf Model. 2010 Oct 25;50(10):1855-64. doi: 10.1021/ci900463u.

PMID:
20968314
12.

Decoys for docking.

Graves AP, Brenk R, Shoichet BK.

J Med Chem. 2005 Jun 2;48(11):3714-28.

13.

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
14.

Evaluation of docking performance: comparative data on docking algorithms.

Kontoyianni M, McClellan LM, Sokol GS.

J Med Chem. 2004 Jan 29;47(3):558-65.

PMID:
14736237
15.

Consensus scoring criteria for improving enrichment in virtual screening.

Yang JM, Chen YF, Shen TW, Kristal BS, Hsu DF.

J Chem Inf Model. 2005 Jul-Aug;45(4):1134-46.

PMID:
16045308
16.

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
17.

G-protein coupled receptors virtual screening using genetic algorithm focused chemical space.

Sage C, Wang R, Jones G.

J Chem Inf Model. 2011 Aug 22;51(8):1754-61. doi: 10.1021/ci200043z. Epub 2011 Jul 27.

PMID:
21761904
18.

SeleX-CS: a new consensus scoring algorithm for hit discovery and lead optimization.

Bar-Haim S, Aharon A, Ben-Moshe T, Marantz Y, Senderowitz H.

J Chem Inf Model. 2009 Mar;49(3):623-33. doi: 10.1021/ci800335j.

PMID:
19231809
19.

Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening.

Hsieh JH, Wang XS, Teotico D, Golbraikh A, Tropsha A.

J Comput Aided Mol Des. 2008 Sep;22(9):593-609. doi: 10.1007/s10822-008-9199-2. Epub 2008 Mar 13.

PMID:
18338225
20.

DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets.

Cereto-Massagué A, Guasch L, Valls C, Mulero M, Pujadas G, Garcia-Vallvé S.

Bioinformatics. 2012 Jun 15;28(12):1661-2. doi: 10.1093/bioinformatics/bts249. Epub 2012 Apr 26.

PMID:
22539671

Supplemental Content

Support Center