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Items: 1 to 20 of 196

1.

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. doi: 10.1002/prot.22457.

PMID:
19452553
2.

Distance-dependent atomic knowledge-based force in protein fold recognition.

Mirzaie M, Sadeghi M.

Proteins. 2012 Mar;80(3):683-90. doi: 10.1002/prot.24011. Epub 2012 Jan 9.

PMID:
22231226
3.

Discrimination of native protein structures using atom-atom contact scoring.

McConkey BJ, Sobolev V, Edelman M.

Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3215-20. Epub 2003 Mar 11.

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5.

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.

6.

Novel nonlinear knowledge-based mean force potentials based on machine learning.

Dong Q, Zhou S.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):476-86. doi: 10.1109/TCBB.2010.86.

PMID:
20820079
7.

Distance dependent centroid to centroid force fields using high resolution decoys.

Rajgaria R, McAllister SR, Floudas CA.

Proteins. 2008 Feb 15;70(3):950-70.

PMID:
17847088
8.

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.

9.

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

Betancourt MR.

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

PMID:
14635131
10.

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
12.

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
13.

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
14.

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
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18.

A pairwise residue contact area-based mean force potential for discrimination of native protein structure.

Arab S, Sadeghi M, Eslahchi C, Pezeshk H, Sheari A.

BMC Bioinformatics. 2010 Jan 9;11:16. doi: 10.1186/1471-2105-11-16.

19.

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.

Randall A, Baldi P.

BMC Struct Biol. 2008 Dec 3;8:52. doi: 10.1186/1472-6807-8-52.

20.

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
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