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Results: 1 to 20 of 144

1.

Use of experimental design to optimize docking performance: the case of LiGenDock, the docking module of LiGen, a new de novo design program.

Beato C, Beccari AR, Cavazzoni C, Lorenzi S, Costantino G.

J Chem Inf Model. 2013 Jun 24;53(6):1503-17. doi: 10.1021/ci400079k. Epub 2013 Apr 30.

PMID:
23590204
[PubMed - indexed for MEDLINE]
2.

LiGen: a high performance workflow for chemistry driven de novo design.

Beccari AR, Cavazzoni C, Beato C, Costantino G.

J Chem Inf Model. 2013 Jun 24;53(6):1518-27. doi: 10.1021/ci400078g. Epub 2013 May 28.

PMID:
23617275
[PubMed - indexed for MEDLINE]
3.

Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a public library of challenging docking benchmark sets.

Bauer MR, Ibrahim TM, Vogel SM, Boeckler FM.

J Chem Inf Model. 2013 Jun 24;53(6):1447-62. doi: 10.1021/ci400115b. Epub 2013 Jun 12.

PMID:
23705874
[PubMed - indexed for MEDLINE]
4.

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
[PubMed - indexed for MEDLINE]
5.

Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C.

J Chem Inf Model. 2009 Jun;49(6):1455-74. doi: 10.1021/ci900056c.

PMID:
19476350
[PubMed - indexed for MEDLINE]
6.

AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.

Pencheva T, Lagorce D, Pajeva I, Villoutreix BO, Miteva MA.

BMC Bioinformatics. 2008 Oct 16;9:438. doi: 10.1186/1471-2105-9-438.

PMID:
18925937
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Consensus docking: improving the reliability of docking in a virtual screening context.

Houston DR, Walkinshaw MD.

J Chem Inf Model. 2013 Feb 25;53(2):384-90. doi: 10.1021/ci300399w. Epub 2013 Feb 7.

PMID:
23351099
[PubMed - indexed for MEDLINE]
8.

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
[PubMed - indexed for MEDLINE]
9.

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.

Perola E, Walters WP, Charifson PS.

Proteins. 2004 Aug 1;56(2):235-49.

PMID:
15211508
[PubMed - indexed for MEDLINE]
10.

FRED and HYBRID docking performance on standardized datasets.

McGann M.

J Comput Aided Mol Des. 2012 Aug;26(8):897-906. doi: 10.1007/s10822-012-9584-8. Epub 2012 Jun 5.

PMID:
22669221
[PubMed - indexed for MEDLINE]
11.

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. Epub 2006 Dec 6.

PMID:
17149653
[PubMed - indexed for MEDLINE]
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.

Multiple structures for virtual ligand screening: defining binding site properties-based criteria to optimize the selection of the query.

Ben Nasr N, Guillemain H, Lagarde N, Zagury JF, Montes M.

J Chem Inf Model. 2013 Feb 25;53(2):293-311. doi: 10.1021/ci3004557. Epub 2013 Jan 29.

PMID:
23312043
[PubMed - indexed for MEDLINE]
14.

FIPSDock: a new molecular docking technique driven by fully informed swarm optimization algorithm.

Liu Y, Zhao L, Li W, Zhao D, Song M, Yang Y.

J Comput Chem. 2013 Jan 5;34(1):67-75. doi: 10.1002/jcc.23108. Epub 2012 Sep 7.

PMID:
22961860
[PubMed - indexed for MEDLINE]
15.

Critical assessment of the automated AutoDock as a new docking tool for virtual screening.

Park H, Lee J, Lee S.

Proteins. 2006 Nov 15;65(3):549-54.

PMID:
16988956
[PubMed - indexed for MEDLINE]
16.

How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces?

Krüger DM, Jessen G, Gohlke H.

J Chem Inf Model. 2012 Nov 26;52(11):2807-11. doi: 10.1021/ci3003599. Epub 2012 Oct 30.

PMID:
23072688
[PubMed - indexed for MEDLINE]
17.

pso@autodock: a fast flexible molecular docking program based on Swarm intelligence.

Namasivayam V, Günther R.

Chem Biol Drug Des. 2007 Dec;70(6):475-84. Epub 2007 Nov 6.

PMID:
17986206
[PubMed - indexed for MEDLINE]
18.

Evaluations of molecular docking programs for virtual screening.

Onodera K, Satou K, Hirota H.

J Chem Inf Model. 2007 Jul-Aug;47(4):1609-18. Epub 2007 Jun 28.

PMID:
17602548
[PubMed - indexed for MEDLINE]
19.

Improving molecular docking through eHiTS' tunable scoring function.

Ravitz O, Zsoldos Z, Simon A.

J Comput Aided Mol Des. 2011 Nov;25(11):1033-51. doi: 10.1007/s10822-011-9482-5. Epub 2011 Nov 11.

PMID:
22076470
[PubMed - indexed for MEDLINE]
20.

Surflex-Dock: Docking benchmarks and real-world application.

Spitzer R, Jain AN.

J Comput Aided Mol Des. 2012 Jun;26(6):687-99. doi: 10.1007/s10822-011-9533-y. Epub 2012 May 9.

PMID:
22569590
[PubMed - indexed for MEDLINE]
Free PMC Article

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