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Results: 1 to 20 of 101

1.

Large-scale reverse docking profiles and their applications.

Lee M, Kim D.

BMC Bioinformatics. 2012;13 Suppl 17:S6. doi: 10.1186/1471-2105-13-S17-S6. Epub 2012 Dec 13.

PMID:
23282219
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.

Estrada T, Zhang B, Cicotti P, Armen RS, Taufer M.

Comput Biol Med. 2012 Jul;42(7):758-71. doi: 10.1016/j.compbiomed.2012.05.001. Epub 2012 Jun 2.

PMID:
22658682
[PubMed - indexed for MEDLINE]
3.

PDTD: a web-accessible protein database for drug target identification.

Gao Z, Li H, Zhang H, Liu X, Kang L, Luo X, Zhu W, Chen K, Wang X, Jiang H.

BMC Bioinformatics. 2008 Feb 19;9:104. doi: 10.1186/1471-2105-9-104.

PMID:
18282303
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Importance of molecular computer modeling in anticancer drug development.

Geromichalos GD.

J BUON. 2007 Sep;12 Suppl 1:S101-18. Review.

PMID:
17935268
[PubMed - indexed for MEDLINE]
5.

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
[PubMed - indexed for MEDLINE]
6.

A large-scale computational approach to drug repositioning.

Li YY, An J, Jones SJ.

Genome Inform. 2006;17(2):239-47.

PMID:
17503396
[PubMed - indexed for MEDLINE]
7.

Potential and limitations of ensemble docking.

Korb O, Olsson TS, Bowden SJ, Hall RJ, Verdonk ML, Liebeschuetz JW, Cole JC.

J Chem Inf Model. 2012 May 25;52(5):1262-74. doi: 10.1021/ci2005934. Epub 2012 Apr 17.

PMID:
22482774
[PubMed - indexed for MEDLINE]
8.

FINDSITE: a threading-based approach to ligand homology modeling.

Brylinski M, Skolnick J.

PLoS Comput Biol. 2009 Jun;5(6):e1000405. doi: 10.1371/journal.pcbi.1000405. Epub 2009 Jun 5.

PMID:
19503616
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Computational methodologies for compound database searching that utilize experimental protein-ligand interaction information.

Tan L, Batista J, Bajorath J.

Chem Biol Drug Des. 2010 Sep 1;76(3):191-200. doi: 10.1111/j.1747-0285.2010.01007.x. Epub 2010 Jul 15. Review.

PMID:
20636330
[PubMed - indexed for MEDLINE]
10.

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach.

Wang JC, Chu PY, Chen CM, Lin JH.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W393-9. doi: 10.1093/nar/gks496. Epub 2012 May 30.

PMID:
22649057
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

[Docking method for drug discovery].

Hirayama N.

Yakugaku Zasshi. 2007 Jan;127(1):113-22. Review. Japanese.

PMID:
17202791
[PubMed - indexed for MEDLINE]
Free Article
12.

Large-scale integrated super-computing platform for next generation virtual drug discovery.

Mitchell W, Matsumoto S.

Curr Opin Chem Biol. 2011 Aug;15(4):553-9. doi: 10.1016/j.cbpa.2011.06.005. Epub 2011 Jun 30. Review.

PMID:
21723773
[PubMed - indexed for MEDLINE]
13.

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide.

Kawatkar S, Wang H, Czerminski R, Joseph-McCarthy D.

J Comput Aided Mol Des. 2009 Aug;23(8):527-39. doi: 10.1007/s10822-009-9281-4. Epub 2009 Jun 3.

PMID:
19495993
[PubMed - indexed for MEDLINE]
14.

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
15.

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
[PubMed - indexed for MEDLINE]
16.

Progressive docking: a hybrid QSAR/docking approach for accelerating in silico high throughput screening.

Cherkasov A, Ban F, Li Y, Fallahi M, Hammond GL.

J Med Chem. 2006 Dec 14;49(25):7466-78.

PMID:
17149875
[PubMed - indexed for MEDLINE]
17.

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery.

Xie L, Xie L, Bourne PE.

Bioinformatics. 2009 Jun 15;25(12):i305-12. doi: 10.1093/bioinformatics/btp220.

PMID:
19478004
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Computational identification of proteins for selectivity assays.

Yoon S, Smellie A, Hartsough D, Filikov A.

Proteins. 2005 May 15;59(3):434-43.

PMID:
15770646
[PubMed - indexed for MEDLINE]
19.

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
20.

Computational resources for protein modelling and drug discovery applications.

Dhaliwal B, Chen YW.

Infect Disord Drug Targets. 2009 Nov;9(5):557-62. Review.

PMID:
19594423
[PubMed - indexed for MEDLINE]

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