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Results: 1 to 20 of 109

Similar articles for PubMed (Select 24410429)

1.

Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design.

Allen WJ, Rizzo RC.

J Chem Inf Model. 2014 Feb 24;54(2):518-29. doi: 10.1021/ci400534h. Epub 2014 Jan 29.

2.

DOCK 6: Impact of new features and current docking performance.

Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC.

J Comput Chem. 2015 Jun 5;36(15):1132-56. doi: 10.1002/jcc.23905.

PMID:
25914306
3.

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. Epub 2009 Oct 13.

PMID:
19823881
4.

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
5.

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
6.

Similarity-driven flexible ligand docking.

Fradera X, Knegtel RM, Mestres J.

Proteins. 2000 Sep 1;40(4):623-36.

PMID:
10899786
7.

MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.

Sauton N, Lagorce D, Villoutreix BO, Miteva MA.

BMC Bioinformatics. 2008 Apr 10;9:184. doi: 10.1186/1471-2105-9-184.

8.

Strategies for lead discovery: application of footprint similarity targeting HIVgp41.

Holden PM, Allen WJ, Gochin M, Rizzo RC.

Bioorg Med Chem. 2014 Jan 1;22(1):651-61. doi: 10.1016/j.bmc.2013.10.022. Epub 2013 Oct 26.

9.

PSI-DOCK: towards highly efficient and accurate flexible ligand docking.

Pei J, Wang Q, Liu Z, Li Q, Yang K, Lai L.

Proteins. 2006 Mar 1;62(4):934-46.

PMID:
16395666
10.

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
11.
12.

A python-based docking program utilizing a receptor bound ligand shape: PythDock.

Chung JY, Cho SJ, Hah JM.

Arch Pharm Res. 2011 Sep;34(9):1451-8. doi: 10.1007/s12272-011-0906-5. Epub 2011 Oct 6.

PMID:
21975806
13.

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
14.

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
15.

Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41.

Balius TE, Allen WJ, Mukherjee S, Rizzo RC.

J Comput Chem. 2013 May 30;34(14):1226-40. doi: 10.1002/jcc.23245. Epub 2013 Feb 22.

16.

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
17.

In silico fragment-based drug discovery: setup and validation of a fragment-to-lead computational protocol using S4MPLE.

Hoffer L, Renaud JP, Horvath D.

J Chem Inf Model. 2013 Apr 22;53(4):836-51. doi: 10.1021/ci4000163. Epub 2013 Apr 11.

PMID:
23537132
18.

Lead Finder docking and virtual screening evaluation with Astex and DUD test sets.

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

J Comput Aided Mol Des. 2012 Jun;26(6):725-35. doi: 10.1007/s10822-012-9549-y. Epub 2012 May 9.

PMID:
22569592
19.

GPU acceleration of Dock6's Amber scoring computation.

Yang H, Zhou Q, Li B, Wang Y, Luan Z, Qian D, Li H.

Adv Exp Med Biol. 2010;680:497-511. doi: 10.1007/978-1-4419-5913-3_56.

PMID:
20865535
20.
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