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Items: 1 to 20 of 27


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.


Conserved residue clusters at protein-protein interfaces and their use in binding site identification.

Guharoy M, Chakrabarti P.

BMC Bioinformatics. 2010 May 27;11:286. doi: 10.1186/1471-2105-11-286.


Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response.

Heo M, Shakhnovich EI.

PLoS Comput Biol. 2010 Mar 12;6(3):e1000710. doi: 10.1371/journal.pcbi.1000710.


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.


Emergence of species in evolutionary "simulated annealing".

Heo M, Kang L, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1869-74. doi: 10.1073/pnas.0809852106. Epub 2009 Jan 22.


Predicting cellular growth from gene expression signatures.

Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG.

PLoS Comput Biol. 2009 Jan;5(1):e1000257. doi: 10.1371/journal.pcbi.1000257. Epub 2009 Jan 2.


Protein-protein interaction and quaternary structure.

Janin J, Bahadur RP, Chakrabarti P.

Q Rev Biophys. 2008 May;41(2):133-80. doi: 10.1017/S0033583508004708. Review.


Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.

Zhang J, Maslov S, Shakhnovich EI.

Mol Syst Biol. 2008;4:210. doi: 10.1038/msb.2008.48. Epub 2008 Aug 5.


Principles of protein-protein interactions: what are the preferred ways for proteins to interact?

Keskin O, Gursoy A, Ma B, Nussinov R.

Chem Rev. 2008 Apr;108(4):1225-44. doi: 10.1021/cr040409x. Epub 2008 Mar 21. Review. No abstract available.


Protein abundance profiling of the Escherichia coli cytosol.

Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D.

BMC Genomics. 2008 Feb 27;9:102. doi: 10.1186/1471-2164-9-102.


The BioGRID Interaction Database: 2008 update.

Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40. Epub 2007 Nov 13.


Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.

Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D.

Mol Biol Cell. 2008 Jan;19(1):352-67. Epub 2007 Oct 24.


Robust protein protein interactions in crowded cellular environments.

Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14952-7. Epub 2007 Sep 11.


A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI.

PLoS Comput Biol. 2007 Jul;3(7):e139.


Positive and negative design in stability and thermal adaptation of natural proteins.

Berezovsky IN, Zeldovich KB, Shakhnovich EI.

PLoS Comput Biol. 2007 Mar 23;3(3):e52. Epub 2007 Feb 1.


Relating three-dimensional structures to protein networks provides evolutionary insights.

Kim PM, Lu LJ, Xia Y, Gerstein MB.

Science. 2006 Dec 22;314(5807):1938-41. Erratum in: Science. 2007 Jan 12;315(5809):187. Science. 2013 Feb 15;339(6121):757.


Structural similarity enhances interaction propensity of proteins.

Lukatsky DB, Shakhnovich BE, Mintseris J, Shakhnovich EI.

J Mol Biol. 2007 Feb 2;365(5):1596-606. Epub 2006 Nov 10.


A simple physical model for scaling in protein-protein interaction networks.

Deeds EJ, Ashenberg O, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):311-6. Epub 2005 Dec 29.


BioGRID: a general repository for interaction datasets.

Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9.


Flexible nets. The roles of intrinsic disorder in protein interaction networks.

Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN.

FEBS J. 2005 Oct;272(20):5129-48. Review.

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