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Items: 1 to 20 of 241

1.

MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm.

Chang DT, Oyang YJ, Lin JH.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W233-8.

2.

ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures.

Chang DT, Chen CY, Chung WC, Oyang YJ, Juan HF, Huang HC.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W76-82.

3.

Protemot: prediction of protein binding sites with automatically extracted geometrical templates.

Chang DT, Weng YZ, Lin JH, Hwang MJ, Oyang YJ.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W303-9.

4.

SODOCK: swarm optimization for highly flexible protein-ligand docking.

Chen HM, Liu BF, Huang HL, Hwang SF, Ho SY.

J Comput Chem. 2007 Jan 30;28(2):612-23.

PMID:
17186483
5.

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach.

Liu X, Ouyang S, Yu B, Liu Y, Huang K, Gong J, Zheng S, Li Z, Li H, Jiang H.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W609-14. doi: 10.1093/nar/gkq300. Epub 2010 Apr 29.

6.

LigDockCSA: protein-ligand docking using conformational space annealing.

Shin WH, Heo L, Lee J, Ko J, Seok C, Lee J.

J Comput Chem. 2011 Nov 30;32(15):3226-32. doi: 10.1002/jcc.21905. Epub 2011 Aug 12.

PMID:
21837636
7.

SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome.

Yang L, Luo H, Chen J, Xing Q, He L.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W406-12. doi: 10.1093/nar/gkp312. Epub 2009 May 5.

8.

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.

9.

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
10.

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites.

Xie ZR, Liu CK, Hsiao FC, Yao A, Hwang MJ.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W292-6. doi: 10.1093/nar/gkt300. Epub 2013 Apr 22.

11.

SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.

Lee PH, Kuo KL, Chu PY, Liu EM, Lin JH.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W559-64. doi: 10.1093/nar/gkp359. Epub 2009 May 11.

12.

Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm.

Gáspári Z, Vlahovicek K, Pongor S.

Bioinformatics. 2005 Aug 1;21(15):3322-3. Epub 2005 May 24.

PMID:
15914542
13.

CovalentDock Cloud: a web server for automated covalent docking.

Ouyang X, Zhou S, Ge Z, Li R, Kwoh CK.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W329-32. doi: 10.1093/nar/gkt406. Epub 2013 May 15.

14.

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles.

Xie ZR, Hwang MJ.

Bioinformatics. 2012 Jun 15;28(12):1579-85. doi: 10.1093/bioinformatics/bts182. Epub 2012 Apr 11.

PMID:
22495747
15.

GalaxySite: ligand-binding-site prediction by using molecular docking.

Heo L, Shin WH, Lee MS, Seok C.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W210-4. doi: 10.1093/nar/gku321. Epub 2014 Apr 21.

16.

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
17.

EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.

Grosdidier A, Zoete V, Michielin O.

Proteins. 2007 Jun 1;67(4):1010-25.

PMID:
17380512
18.

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
20.

PiDNA: Predicting protein-DNA interactions with structural models.

Lin CK, Chen CY.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W523-30. doi: 10.1093/nar/gkt388. Epub 2013 May 22.

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