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Results: 1 to 20 of 81

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.

PMID:
18930732
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
17468399
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions.

Jothi R, Cherukuri PF, Tasneem A, Przytycka TM.

J Mol Biol. 2006 Sep 29;362(4):861-75. Epub 2006 Aug 1.

PMID:
16949097
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
24349035
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
[PubMed - indexed for MEDLINE]
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
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
23217198
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
16606443
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
[PubMed - indexed for MEDLINE]
Free Article
11.

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
[PubMed - indexed for MEDLINE]
Free Article
12.

Evolutionary rates at codon sites may be used to align sequences and infer protein domain function.

Durand PM, Hazelhurst S, Coetzer TL.

BMC Bioinformatics. 2010 Mar 24;11:151. doi: 10.1186/1471-2105-11-151.

PMID:
20334658
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
18818697
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
19329067
[PubMed - indexed for MEDLINE]
Free Article
15.

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
[PubMed - indexed for MEDLINE]
Free Article
16.

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
[PubMed - indexed for MEDLINE]
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.

PMID:
19165315
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
[PubMed - indexed for MEDLINE]
19.

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.

PMID:
17517763
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Statistical analysis of domains in interacting protein pairs.

Nye TM, Berzuini C, Gilks WR, Babu MM, Teichmann SA.

Bioinformatics. 2005 Apr 1;21(7):993-1001. Epub 2004 Oct 27.

PMID:
15509600
[PubMed - indexed for MEDLINE]
Free Article
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