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Items: 1 to 20 of 74

1.

Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks.

Johnson ME, Hummer G.

Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):603-8. doi: 10.1073/pnas.1010954108. Epub 2010 Dec 27.

2.

Evolutionary cores of domain co-occurrence networks.

Wuchty S, Almaas E.

BMC Evol Biol. 2005 Mar 23;5:24.

3.

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M.

Bioinformatics. 2005 Jun;21 Suppl 1:i302-10.

PMID:
15961472
4.

Exploiting amino acid composition for predicting protein-protein interactions.

Roy S, Martinez D, Platero H, Lane T, Werner-Washburne M.

PLoS One. 2009 Nov 20;4(11):e7813. doi: 10.1371/journal.pone.0007813.

5.

Evolutionary capacitance and control of protein stability in protein-protein interaction networks.

Dixit PD, Maslov S.

PLoS Comput Biol. 2013 Apr;9(4):e1003023. doi: 10.1371/journal.pcbi.1003023. Epub 2013 Apr 4.

6.
7.

A kinetic model of the evolution of a protein interaction network.

Pawlowski PH, Kaczanowski S, Zielenkiewicz P.

BMC Genomics. 2013 Mar 14;14:172. doi: 10.1186/1471-2164-14-172.

8.

Oligomeric protein structure networks: insights into protein-protein interactions.

Brinda KV, Vishveshwara S.

BMC Bioinformatics. 2005 Dec 10;6:296.

9.

C. elegans: an invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway.

Paik YK, Jeong SK, Lee EY, Jeong PY, Shim YH.

Expert Rev Proteomics. 2006 Aug;3(4):439-53. Review.

PMID:
16901202
10.

I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions.

Tackett AJ, DeGrasse JA, Sekedat MD, Oeffinger M, Rout MP, Chait BT.

J Proteome Res. 2005 Sep-Oct;4(5):1752-6.

PMID:
16212429
11.

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M.

Genome Res. 2004 Jun;14(6):1107-18.

12.

Characterization of degree frequency distribution in protein interaction networks.

Romano SA, Eguia MC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Mar;71(3 Pt 1):031901. Epub 2005 Mar 3.

PMID:
15903453
13.

Effect of sampling on topology predictions of protein-protein interaction networks.

Han JD, Dupuy D, Bertin N, Cusick ME, Vidal M.

Nat Biotechnol. 2005 Jul;23(7):839-44.

PMID:
16003372
14.
15.

Proteome-wide protein interaction measurements of bacterial proteins of unknown function.

Meier M, Sit RV, Quake SR.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):477-82. doi: 10.1073/pnas.1210634110. Epub 2012 Dec 24.

16.

ProtNet: a tool for stochastic simulations of protein interaction networks dynamics.

Bernaschi M, Castiglione F, Ferranti A, Gavrila C, Tinti M, Cesareni G.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S4.

17.

Construction of functional interaction networks through consensus localization predictions of the human proteome.

Park S, Yang JS, Jang SK, Kim S.

J Proteome Res. 2009 Jul;8(7):3367-76. doi: 10.1021/pr900018z.

PMID:
19415893
18.

Pairwise alignment of protein interaction networks.

Koyut├╝rk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A.

J Comput Biol. 2006 Mar;13(2):182-99.

PMID:
16597234
19.

Small-world network approach to identify key residues in protein-protein interaction.

del Sol A, O'Meara P.

Proteins. 2005 Feb 15;58(3):672-82.

PMID:
15617065
20.

Energetic determinants of protein binding specificity: insights into protein interaction networks.

Carbonell P, Nussinov R, del Sol A.

Proteomics. 2009 Apr;9(7):1744-53. doi: 10.1002/pmic.200800425.

PMID:
19253304

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