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Items: 1 to 20 of 87

1.

Correlated evolution of interacting proteins: looking behind the mirrortree.

Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM.

J Mol Biol. 2009 Jan 9;385(1):91-8. doi: 10.1016/j.jmb.2008.09.078. Epub 2008 Oct 9.

2.

Predicting protein-protein interaction by the mirrortree method: possibilities and limitations.

Zhou H, Jakobsson E.

PLoS One. 2013 Dec 13;8(12):e81100. doi: 10.1371/journal.pone.0081100. eCollection 2013.

3.

Specificity in protein interactions and its relationship with sequence diversity and coevolution.

Hakes L, Lovell SC, Oliver SG, Robertson DL.

Proc Natl Acad Sci U S A. 2007 May 8;104(19):7999-8004. Epub 2007 Apr 27.

4.

Prediction of protein interaction based on similarity of phylogenetic trees.

Pazos F, Juan D, Izarzugaza JM, Leon E, Valencia A.

Methods Mol Biol. 2008;484:523-35. doi: 10.1007/978-1-59745-398-1_31.

PMID:
18592199
5.
6.

Predicting protein domain interactions from coevolution of conserved regions.

Kann MG, Jothi R, Cherukuri PF, Przytycka TM.

Proteins. 2007 Jun 1;67(4):811-20.

PMID:
17357158
7.

Exploiting the co-evolution of interacting proteins to discover interaction specificity.

Ramani AK, Marcotte EM.

J Mol Biol. 2003 Mar 14;327(1):273-84.

PMID:
12614624
8.

The origins of the evolutionary signal used to predict protein-protein interactions.

Swapna LS, Srinivasan N, Robertson DL, Lovell SC.

BMC Evol Biol. 2012 Dec 6;12:238. doi: 10.1186/1471-2148-12-238.

9.

Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).

Kim WK, Bolser DM, Park JH.

Bioinformatics. 2004 May 1;20(7):1138-50. Epub 2004 Feb 5.

PMID:
14764552
10.

Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins.

Hesselberth JR, Miller JP, Golob A, Stajich JE, Michaud GA, Fields S.

Genome Biol. 2006;7(4):R30. Epub 2006 Apr 10.

11.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

Ochoa D, García-Gutiérrez P, Juan D, Valencia A, Pazos F.

Mol Biosyst. 2013 Jan 27;9(1):70-6. doi: 10.1039/c2mb25325a. Epub 2012 Oct 26.

PMID:
23104128
12.

Interactome-wide prediction of protein-protein binding sites reveals effects of protein sequence variation in Arabidopsis thaliana.

Leal Valentim F, Neven F, Boyen P, van Dijk AD.

PLoS One. 2012;7(10):e47022. doi: 10.1371/journal.pone.0047022. Epub 2012 Oct 15.

13.

Equivalent binding sites reveal convergently evolved interaction motifs.

Henschel A, Kim WK, Schroeder M.

Bioinformatics. 2006 Mar 1;22(5):550-5. Epub 2005 Nov 15.

PMID:
16287935
14.

Using coevolution to predict protein-protein interactions.

Clark GW, Dar VU, Bezginov A, Yang JM, Charlebois RL, Tillier ER.

Methods Mol Biol. 2011;781:237-56. doi: 10.1007/978-1-61779-276-2_11.

PMID:
21877284
15.

Protein co-evolution, co-adaptation and interactions.

Pazos F, Valencia A.

EMBO J. 2008 Oct 22;27(20):2648-55. doi: 10.1038/emboj.2008.189. Epub 2008 Sep 25. Review.

16.

Structure-templated predictions of novel protein interactions from sequence information.

Betel D, Breitkreuz KE, Isserlin R, Dewar-Darch D, Tyers M, Hogue CW.

PLoS Comput Biol. 2007 Sep;3(9):1783-9.

17.

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.

18.

An integrated view of molecular coevolution in protein-protein interactions.

Lovell SC, Robertson DL.

Mol Biol Evol. 2010 Nov;27(11):2567-75. doi: 10.1093/molbev/msq144. Epub 2010 Jun 14. Review.

PMID:
20551042
19.

Identification of semaphorin 5A interacting protein by applying apriori knowledge and peptide complementarity related to protein evolution and structure.

Sadanandam A, Varney ML, Singh RK.

Genomics Proteomics Bioinformatics. 2008 Dec;6(3-4):163-74. doi: 10.1016/S1672-0229(09)60004-8.

20.

3D-partner: a web server to infer interacting partners and binding models.

Chen YC, Lo YS, Hsu WC, Yang JM.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W561-7. Epub 2007 May 21.

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