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Results: 1 to 20 of 169

1.

A graph-theory algorithm for rapid protein side-chain prediction.

Canutescu AA, Shelenkov AA, Dunbrack RL Jr.

Protein Sci. 2003 Sep;12(9):2001-14.

PMID:
12930999
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Improved prediction of protein side-chain conformations with SCWRL4.

Krivov GG, Shapovalov MV, Dunbrack RL Jr.

Proteins. 2009 Dec;77(4):778-95. doi: 10.1002/prot.22488.

PMID:
19603484
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library.

Peterson RW, Dutton PL, Wand AJ.

Protein Sci. 2004 Mar;13(3):735-51.

PMID:
14978310
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.

Mendes J, Nagarajaram HA, Soares CM, Blundell TL, Carrondo MA.

Biopolymers. 2001 Aug;59(2):72-86.

PMID:
11373721
[PubMed - indexed for MEDLINE]
5.
6.

SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations.

Nagata K, Randall A, Baldi P.

Proteins. 2012 Jan;80(1):142-53. doi: 10.1002/prot.23170. Epub 2011 Nov 9.

PMID:
22072531
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Residue-rotamer-reduction algorithm for the protein side-chain conformation problem.

Xie W, Sahinidis NV.

Bioinformatics. 2006 Jan 15;22(2):188-94. Epub 2005 Nov 8.

PMID:
16278239
[PubMed - indexed for MEDLINE]
Free Article
8.

A protein-dependent side-chain rotamer library.

Bhuyan MS, Gao X.

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S10. doi: 10.1186/1471-2105-12-S14-S10.

PMID:
22373394
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Side-chain modeling with an optimized scoring function.

Liang S, Grishin NV.

Protein Sci. 2002 Feb;11(2):322-31.

PMID:
11790842
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.

Hartmann C, Antes I, Lengauer T.

Protein Sci. 2007 Jul;16(7):1294-307. Epub 2007 Jun 13.

PMID:
17567749
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.

Bower MJ, Cohen FE, Dunbrack RL Jr.

J Mol Biol. 1997 Apr 18;267(5):1268-82.

PMID:
9150411
[PubMed - indexed for MEDLINE]
12.

OPUS-Rota: a fast and accurate method for side-chain modeling.

Lu M, Dousis AD, Ma J.

Protein Sci. 2008 Sep;17(9):1576-85. doi: 10.1110/ps.035022.108. Epub 2008 Jun 12.

PMID:
18556476
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Optimization of van der Waals energy for protein side-chain placement and design.

Fahmy A, Wagner G.

Biophys J. 2011 Oct 5;101(7):1690-8. doi: 10.1016/j.bpj.2011.07.052.

PMID:
21961595
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets.

Camacho CJ.

Proteins. 2005 Aug 1;60(2):245-51.

PMID:
15981253
[PubMed - indexed for MEDLINE]
15.

TOUCHSTONE II: a new approach to ab initio protein structure prediction.

Zhang Y, Kolinski A, Skolnick J.

Biophys J. 2003 Aug;85(2):1145-64.

PMID:
12885659
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Extending the accuracy limits of prediction for side-chain conformations.

Xiang Z, Honig B.

J Mol Biol. 2001 Aug 10;311(2):421-30. Erratum in: J Mol Biol 2001 Sep 14;312(2):419.

PMID:
11478870
[PubMed - indexed for MEDLINE]
17.

Protein design using continuous rotamers.

Gainza P, Roberts KE, Donald BR.

PLoS Comput Biol. 2012 Jan;8(1):e1002335. doi: 10.1371/journal.pcbi.1002335. Epub 2012 Jan 12.

PMID:
22279426
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Modeling side-chain conformation for homologous proteins using an energy-based rotamer search.

Wilson C, Gregoret LM, Agard DA.

J Mol Biol. 1993 Feb 20;229(4):996-1006.

PMID:
8445659
[PubMed - indexed for MEDLINE]
19.

LOOPER: a molecular mechanics-based algorithm for protein loop prediction.

Spassov VZ, Flook PK, Yan L.

Protein Eng Des Sel. 2008 Feb;21(2):91-100. doi: 10.1093/protein/gzm083. Epub 2008 Jan 14.

PMID:
18194981
[PubMed - indexed for MEDLINE]
Free Article
20.

Backbone-dependent rotamer library for proteins. Application to side-chain prediction.

Dunbrack RL Jr, Karplus M.

J Mol Biol. 1993 Mar 20;230(2):543-74.

PMID:
8464064
[PubMed - indexed for MEDLINE]

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