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Items: 1 to 20 of 105


Protein interface classification by evolutionary analysis.

Duarte JM, Srebniak A, Schärer MA, Capitani G.

BMC Bioinformatics. 2012 Dec 22;13:334. doi: 10.1186/1471-2105-13-334.


A PDB-wide, evolution-based assessment of protein-protein interfaces.

Baskaran K, Duarte JM, Biyani N, Bliven S, Capitani G.

BMC Struct Biol. 2014 Oct 18;14:22. doi: 10.1186/s12900-014-0022-0.


CRK: an evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts.

Schärer MA, Grütter MG, Capitani G.

Proteins. 2010 Sep;78(12):2707-13. doi: 10.1002/prot.22787.


Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts.

Capitani G, Duarte JM, Baskaran K, Bliven S, Somody JC.

Bioinformatics. 2016 Feb 15;32(4):481-9. doi: 10.1093/bioinformatics/btv622. Epub 2015 Oct 27. Review.


Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts.

Liu Q, Li Z, Li J.

BMC Bioinformatics. 2014;15 Suppl 16:S3. doi: 10.1186/1471-2105-15-S16-S3. Epub 2014 Dec 8.


PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein-protein interfaces.

Guharoy M, Pal A, Dasgupta M, Chakrabarti P.

J Struct Funct Genomics. 2011 Mar;12(1):33-41. doi: 10.1007/s10969-011-9108-0. Epub 2011 Apr 26.


Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.

PLoS Comput Biol. 2009 Jan;5(1):e1000267. doi: 10.1371/journal.pcbi.1000267. Epub 2009 Jan 23.


Presaging critical residues in protein interfaces-web server (PCRPi-W): a web server to chart hot spots in protein interfaces.

Segura Mora J, Assi SA, Fernandez-Fuentes N.

PLoS One. 2010 Aug 23;5(8):e12352. doi: 10.1371/journal.pone.0012352.


MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

Cai JJ, Smith DK, Xia X, Yuen KY.

BMC Bioinformatics. 2005 Mar 22;6:64.


PCI-SS: MISO dynamic nonlinear protein secondary structure prediction.

Green JR, Korenberg MJ, Aboul-Magd MO.

BMC Bioinformatics. 2009 Jul 17;10:222. doi: 10.1186/1471-2105-10-222.


HomPPI: a class of sequence homology based protein-protein interface prediction methods.

Xue LC, Dobbs D, Honavar V.

BMC Bioinformatics. 2011 Jun 17;12:244. doi: 10.1186/1471-2105-12-244.


SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces.

Teyra J, Doms A, Schroeder M, Pisabarro MT.

BMC Bioinformatics. 2006 Mar 2;7:104.


SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.


ProFAT: a web-based tool for the functional annotation of protein sequences.

Bradshaw CR, Surendranath V, Habermann B.

BMC Bioinformatics. 2006 Oct 23;7:466.


HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information.

Liu R, Hu J.

BMC Bioinformatics. 2011 May 26;12:207. doi: 10.1186/1471-2105-12-207.


Identification of similar regions of protein structures using integrated sequence and structure analysis tools.

Peters B, Moad C, Youn E, Buffington K, Heiland R, Mooney S.

BMC Struct Biol. 2006 Mar 9;6:4.


DBAC: a simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts.

Li Z, Wong L, Li J.

BMC Syst Biol. 2011 Jun 20;5 Suppl 1:S5. doi: 10.1186/1752-0509-5-S1-S5.


Predicting DNA-binding sites of proteins from amino acid sequence.

Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V.

BMC Bioinformatics. 2006 May 19;7:262.


The many faces of protein-protein interactions: A compendium of interface geometry.

Kim WK, Henschel A, Winter C, Schroeder M.

PLoS Comput Biol. 2006 Sep 29;2(9):e124. Epub 2006 Jul 31.


Conservation and relative importance of residues across protein-protein interfaces.

Guharoy M, Chakrabarti P.

Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15447-52. Epub 2005 Oct 12.

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