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Similar articles for PubMed (Select 19774465)

1.

Computational modelling of protein interactions: energy minimization for the refinement and scoring of association decoys.

Dibrov A, Myal Y, Leygue E.

Acta Biotheor. 2009 Dec;57(4):419-28. doi: 10.1007/s10441-009-9085-x. Epub 2009 Sep 23.

PMID:
19774465
2.

Combination of scoring functions improves discrimination in protein-protein docking.

Murphy J, Gatchell DW, Prasad JC, Vajda S.

Proteins. 2003 Dec 1;53(4):840-54.

PMID:
14635126
3.

Using correlated parameters for improved ranking of protein-protein docking decoys.

Mitra P, Pal D.

J Comput Chem. 2011 Apr 15;32(5):787-96. doi: 10.1002/jcc.21657. Epub 2010 Oct 12.

PMID:
20941737
4.

Scoring docked conformations generated by rigid-body protein-protein docking.

Camacho CJ, Gatchell DW, Kimura SR, Vajda S.

Proteins. 2000 Aug 15;40(3):525-37.

PMID:
10861944
5.

Consensus scoring for enriching near-native structures from protein-protein docking decoys.

Liang S, Meroueh SO, Wang G, Qiu C, Zhou Y.

Proteins. 2009 May 1;75(2):397-403. doi: 10.1002/prot.22252.

6.

MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases.

Del Carpio-Muñoz CA, Ichiishi E, Yoshimori A, Yoshikawa T.

Proteins. 2002 Sep 1;48(4):696-732.

PMID:
12211037
7.

Refining near-native protein-protein docking decoys by local resampling and energy minimization.

Liang S, Wang G, Zhou Y.

Proteins. 2009 Aug 1;76(2):309-16. doi: 10.1002/prot.22343.

8.

Assessing scoring functions for protein-ligand interactions.

Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd.

J Med Chem. 2004 Jun 3;47(12):3032-47.

PMID:
15163185
9.

Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.

Jackson RM, Gabb HA, Sternberg MJ.

J Mol Biol. 1998 Feb 13;276(1):265-85.

PMID:
9514726
10.

ProVal: a protein-scoring function for the selection of native and near-native folds.

Berglund A, Head RD, Welsh EA, Marshall GR.

Proteins. 2004 Feb 1;54(2):289-302.

PMID:
14696191
11.

A reduced protein model with accurate native-structure identification ability.

Betancourt MR.

Proteins. 2003 Dec 1;53(4):889-907.

PMID:
14635131
12.

Recent progress and future directions in protein-protein docking.

Ritchie DW.

Curr Protein Pept Sci. 2008 Feb;9(1):1-15. Review.

PMID:
18336319
13.

Soft protein-protein docking in internal coordinates.

Fernández-Recio J, Totrov M, Abagyan R.

Protein Sci. 2002 Feb;11(2):280-91.

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16.

A new pairwise folding potential based on improved decoy generation and side-chain packing.

Loose C, Klepeis JL, Floudas CA.

Proteins. 2004 Feb 1;54(2):303-14.

PMID:
14696192
17.

A continuum model for protein-protein interactions: application to the docking problem.

Jackson RM, Sternberg MJ.

J Mol Biol. 1995 Jul 7;250(2):258-75.

PMID:
7541840
18.
19.

Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.

Arnautova YA, Vorobjev YN, Vila JA, Scheraga HA.

Proteins. 2009 Oct;77(1):38-51. doi: 10.1002/prot.22414.

PMID:
19384995
20.
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