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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.PMID: 18957132 [PubMed - indexed for MEDLINE]Related articlesFree article

An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

Zhang C, Liu S, Zhou H, Zhou Y.

Protein Sci. 2004 Feb;13(2):400-11.PMID: 14739325 [PubMed - indexed for MEDLINE]Related articlesFree article

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

Betancourt MR.

Proteins. 2003 Dec 1;53(4):889-907.PMID: 14635131 [PubMed - indexed for MEDLINE]Related articles

Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm.

Fang Q, Shortle D.

J Mol Biol. 2006 Jun 23;359(5):1456-67. Epub 2006 Apr 27.PMID: 16678202 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 18181137 [PubMed - indexed for MEDLINE]Related articles

Novel knowledge-based mean force potential at the profile level.

Dong Q, Wang X, Lin L.

BMC Bioinformatics. 2006 Jun 27;7:324.PMID: 16803615 [PubMed - indexed for MEDLINE]Related articlesFree article

Improved protein structure selection using decoy-dependent discriminatory functions.

Wang K, Fain B, Levitt M, Samudrala R.

BMC Struct Biol. 2004 Jun 18;4:8.PMID: 15207004 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving consensus structure by eliminating averaging artifacts.

Dukka BK.

BMC Struct Biol. 2009 Mar 6;9:12.PMID: 19267905 [PubMed - indexed for MEDLINE]Related articlesFree article

Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

Taly JF, Marin A, Gibrat JF.

BMC Bioinformatics. 2008 Jan 7;9:6.PMID: 18179702 [PubMed - indexed for MEDLINE]Related articlesFree article

Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors.

Zhang J, Chen R, Liang J.

Proteins. 2006 Jun 1;63(4):949-60.PMID: 16477624 [PubMed - indexed for MEDLINE]Related articles

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.

Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF.

J Mol Biol. 2006 Nov 3;363(4):835-57. Epub 2006 Aug 18.PMID: 16982067 [PubMed - indexed for MEDLINE]Related articles

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

Lu H, Skolnick J.

Proteins. 2001 Aug 15;44(3):223-32.PMID: 11455595 [PubMed - indexed for MEDLINE]Related articles

A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys.

Mirzaie M, Eslahchi C, Pezeshk H, Sadeghi M.

Proteins. 2009 Nov 1;77(2):454-63.PMID: 19452553 [PubMed - indexed for MEDLINE]Related articles

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 [PubMed - indexed for MEDLINE]Related articles

Scoring predictive models using a reduced representation of proteins: model and energy definition.

Fogolari F, Pieri L, Dovier A, Bortolussi L, Giugliarelli G, Corazza A, Esposito G, Viglino P.

BMC Struct Biol. 2007 Mar 23;7:15.PMID: 17378941 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein structure evaluation using an all-atom energy based empirical scoring function.

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

J Biomol Struct Dyn. 2006 Feb;23(4):385-406.PMID: 16363875 [PubMed - indexed for MEDLINE]Related articlesFree article

A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

Ferrada E, Vergara IA, Melo F.

Cell Biochem Biophys. 2007;49(2):111-24.PMID: 17906366 [PubMed - indexed for MEDLINE]Related articles

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 [PubMed - indexed for MEDLINE]Related articles

Statistically based reduced representation of amino acid side chains.

Rainey JK, Goh MC.

J Chem Inf Comput Sci. 2004 May-Jun;44(3):817-30.PMID: 15154746 [PubMed - indexed for MEDLINE]Related articles

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

Koliński A, Bujnicki JM.

Proteins. 2005;61 Suppl 7:84-90.PMID: 16187348 [PubMed - indexed for MEDLINE]Related articles