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Items: 1 to 20 of 298

1.

KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

Rodrigues JP, Levitt M, Chopra G.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W323-8. doi: 10.1093/nar/gks376. Epub 2012 May 7.

2.

3Drefine: an interactive web server for efficient protein structure refinement.

Bhattacharya D, Nowotny J, Cao R, Cheng J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W406-9. doi: 10.1093/nar/gkw336. Epub 2016 Apr 29.

3.

Consistent refinement of submitted models at CASP using a knowledge-based potential.

Chopra G, Kalisman N, Levitt M.

Proteins. 2010 Sep;78(12):2668-78. doi: 10.1002/prot.22781.

4.

GalaxyWEB server for protein structure prediction and refinement.

Ko J, Park H, Heo L, Seok C.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W294-7. doi: 10.1093/nar/gks493. Epub 2012 May 30.

5.

i3Drefine software for protein 3D structure refinement and its assessment in CASP10.

Bhattacharya D, Cheng J.

PLoS One. 2013 Jul 19;8(7):e69648. doi: 10.1371/journal.pone.0069648. Print 2013.

6.

3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.

Bhattacharya D, Cheng J.

Proteins. 2013 Jan;81(1):119-31. doi: 10.1002/prot.24167. Epub 2012 Sep 26.

7.

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins.

Roche DB, Tetchner SJ, McGuffin LJ.

BMC Bioinformatics. 2011 May 16;12:160. doi: 10.1186/1471-2105-12-160.

8.

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

Ryu H, Lim G, Sung BH, Lee J.

Bioinformatics. 2016 Feb 15;32(4):611-3. doi: 10.1093/bioinformatics/btv595. Epub 2015 Oct 26.

PMID:
26504145
9.

Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.

Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA.

Proteins. 2014 May;82(5):794-814. doi: 10.1002/prot.24459. Epub 2013 Nov 22.

PMID:
24174311
10.

The FALC-Loop web server for protein loop modeling.

Ko J, Lee D, Park H, Coutsias EA, Lee J, Seok C.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W210-4. doi: 10.1093/nar/gkr352. Epub 2011 May 16.

11.

CABS-flex: Server for fast simulation of protein structure fluctuations.

Jamroz M, Kolinski A, Kmiecik S.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W427-31. doi: 10.1093/nar/gkt332. Epub 2013 May 8.

12.

Protinfo PPC: a web server for atomic level prediction of protein complexes.

Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W519-25. doi: 10.1093/nar/gkp306. Epub 2009 May 6.

13.

RosettaBackrub--a web server for flexible backbone protein structure modeling and design.

Lauck F, Smith CA, Friedland GF, Humphris EL, Kortemme T.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W569-75. doi: 10.1093/nar/gkq369. Epub 2010 May 12.

14.

FireDock: a web server for fast interaction refinement in molecular docking.

Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W229-32. doi: 10.1093/nar/gkn186. Epub 2008 Apr 19.

15.

QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.

Benkert P, Schwede T, Tosatto SC.

BMC Struct Biol. 2009 May 20;9:35. doi: 10.1186/1472-6807-9-35.

16.

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

Chen J, Im W, Brooks CL 3rd.

J Am Chem Soc. 2004 Dec 15;126(49):16038-47.

PMID:
15584737
17.

Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment.

Khoury GA, Smadbeck J, Kieslich CA, Koskosidis AJ, Guzman YA, Tamamis P, Floudas CA.

Proteins. 2017 Jun;85(6):1078-1098. doi: 10.1002/prot.25274. Epub 2017 Mar 21.

PMID:
28241391
18.

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.

Arnold K, Bordoli L, Kopp J, Schwede T.

Bioinformatics. 2006 Jan 15;22(2):195-201. Epub 2005 Nov 13.

PMID:
16301204
19.

PepBuild: a web server for building structure data of peptides/proteins.

Singh B.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W559-61.

20.

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