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Items: 1 to 20 of 149

1.

A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues.

Muppirala UK, Li Z.

Protein Eng Des Sel. 2006 Jun;19(6):265-75. Epub 2006 Mar 24.

PMID:
16565147
2.

Spatial profiling of protein hydrophobicity: native vs. decoy structures.

Zhou R, Silverman BD, Royyuru AK, Athma P.

Proteins. 2003 Sep 1;52(4):561-72.

PMID:
12910456
3.

Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction.

Pabuwal V, Li Z.

Protein Eng Des Sel. 2008 Jan;21(1):55-64. doi: 10.1093/protein/gzm059. Epub 2008 Jan 3.

PMID:
18178566
4.

Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations.

Chiu YY, Hwang JK, Yang JM.

J Comput Chem. 2008 Jul 15;29(9):1364-73. doi: 10.1002/jcc.20897.

PMID:
18181137
5.

How well can we predict native contacts in proteins based on decoy structures and their energies?

Zhu J, Zhu Q, Shi Y, Liu H.

Proteins. 2003 Sep 1;52(4):598-608.

PMID:
12910459
6.

Sequence and structural analysis of binding site residues in protein-protein complexes.

Gromiha MM, Yokota K, Fukui K.

Int J Biol Macromol. 2010 Mar 1;46(2):187-92. doi: 10.1016/j.ijbiomac.2009.11.009. Epub 2009 Dec 21.

PMID:
20026105
7.

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
8.

Recognizing native folds by the arrangement of hydrophobic and polar residues.

Huang ES, Subbiah S, Levitt M.

J Mol Biol. 1995 Oct 6;252(5):709-20.

PMID:
7563083
9.

A knowledge-based structure-discriminating function that requires only main-chain atom coordinates.

Makino Y, Itoh N.

BMC Struct Biol. 2008 Oct 29;8:46. doi: 10.1186/1472-6807-8-46.

10.

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

Shamim MT, Anwaruddin M, Nagarajaram HA.

Bioinformatics. 2007 Dec 15;23(24):3320-7. Epub 2007 Nov 7.

PMID:
17989092
11.

Optimizing physical energy functions for protein folding.

Fujitsuka Y, Takada S, Luthey-Schulten ZA, Wolynes PG.

Proteins. 2004 Jan 1;54(1):88-103.

PMID:
14705026
12.

Potential for assessing quality of protein structure based on contact number prediction.

Ishida T, Nakamura S, Shimizu K.

Proteins. 2006 Sep 1;64(4):940-7.

PMID:
16788993
13.

A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set.

Rajgaria R, McAllister SR, Floudas CA.

Proteins. 2006 Nov 15;65(3):726-41.

PMID:
16981202
14.

Hydrophobic moments of protein structures: spatially profiling the distribution.

Silverman BD.

Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4996-5001. Epub 2001 Apr 17.

15.

A computational pathway for bracketing native-like structures fo small alpha helical globular proteins.

Narang P, Bhushan K, Bose S, Jayaram B.

Phys Chem Chem Phys. 2005 Jun 7;7(11):2364-75.

PMID:
19785123
16.

Network properties of protein-decoy structures.

Chatterjee S, Bhattacharyya M, Vishveshwara S.

J Biomol Struct Dyn. 2012;29(6):606-22. doi: 10.1080/07391102.2011.672625.

PMID:
22545992
17.

Three key residues form a critical contact network in a protein folding transition state.

Vendruscolo M, Paci E, Dobson CM, Karplus M.

Nature. 2001 Feb 1;409(6820):641-5.

PMID:
11214326
18.
19.

Inter-residue interactions in protein folding and stability.

Gromiha MM, Selvaraj S.

Prog Biophys Mol Biol. 2004 Oct;86(2):235-77. Review.

PMID:
15288760
20.

Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.

Bastolla U, Ortíz AR, Porto M, Teichert F.

Proteins. 2008 Dec;73(4):872-88. doi: 10.1002/prot.22113.

PMID:
18536008

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