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Items: 1 to 20 of 101

1.

Network properties of decoys and CASP predicted models: a comparison with native protein structures.

Chatterjee S, Ghosh S, Vishveshwara S.

Mol Biosyst. 2013 Jul;9(7):1774-88. doi: 10.1039/c3mb70157c. Epub 2013 May 22.

PMID:
23694935
2.

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
3.

Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.

Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA.

Proteins. 2014 May;82(5):794-814. doi: 10.1002/prot.24459. Epub 2013 Nov 22.

PMID:
24174311
4.

SVR_CAF: an integrated score function for detecting native protein structures among decoys.

Zhou J, Yan W, Hu G, Shen B.

Proteins. 2014 Apr;82(4):556-64. doi: 10.1002/prot.24421. Epub 2013 Oct 17.

PMID:
24115148
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.

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
7.

Atomic interaction networks in the core of protein domains and their native folds.

Soundararajan V, Raman R, Raguram S, Sasisekharan V, Sasisekharan R.

PLoS One. 2010 Feb 23;5(2):e9391. doi: 10.1371/journal.pone.0009391.

8.
9.

SPICKER: a clustering approach to identify near-native protein folds.

Zhang Y, Skolnick J.

J Comput Chem. 2004 Apr 30;25(6):865-71.

PMID:
15011258
10.

Predicting RNA-protein interactions using only sequence information.

Muppirala UK, Honavar VG, Dobbs D.

BMC Bioinformatics. 2011 Dec 22;12:489. doi: 10.1186/1471-2105-12-489.

11.
12.

i3Drefine software for protein 3D structure refinement and its assessment in CASP10.

Bhattacharya D, Cheng J.

PLoS One. 2013 Jul 19;8(7):e69648. doi: 10.1371/journal.pone.0069648. Print 2013.

13.

Improving protein secondary structure prediction using a multi-modal BP method.

Qu W, Sui H, Yang B, Qian W.

Comput Biol Med. 2011 Oct;41(10):946-59. doi: 10.1016/j.compbiomed.2011.08.005. Epub 2011 Aug 30.

PMID:
21880310
14.

Feature-based classification of native and non-native protein-protein interactions: Comparing supervised and semi-supervised learning approaches.

Zhao N, Pang B, Shyu CR, Korkin D.

Proteomics. 2011 Nov;11(22):4321-30. doi: 10.1002/pmic.201100217. Epub 2011 Oct 17.

PMID:
22002942
15.

Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding.

Mishra A, Rao S, Mittal A, Jayaram B.

Biochim Biophys Acta. 2013 Aug;1834(8):1520-31. doi: 10.1016/j.bbapap.2013.04.023. Epub 2013 May 7.

PMID:
23665455
17.

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
18.
19.

Solvent and lipid accessibility prediction as a basis for model quality assessment in soluble and membrane proteins.

Phatak M, Adamczak R, Cao B, Wagner M, Meller J.

Curr Protein Pept Sci. 2011 Sep;12(6):563-73.

PMID:
21787302
20.

Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states.

Shirota M, Ishida T, Kinoshita K.

Proteins. 2011 May;79(5):1550-63. doi: 10.1002/prot.22982. Epub 2011 Mar 1.

PMID:
21365682

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