Pawson T, Nash P: Assembly of cell regulatory systems through protein interaction domains. Science. 2003, 300 (5618): 445-452. 10.1126/science.1083653.
Article
CAS
PubMed
Google Scholar
Pawson T, Linding R: Network medicine. FEBS Lett. 2008, 582: 1266-1270. 10.1016/j.febslet.2008.02.011.
Article
CAS
PubMed
Google Scholar
Alto NM, Shao F, Lazar CS, Brost RL, Chua G, Mattoo S, McMahon SA, Ghosh P, Hughes TR, Boone C, Dixon JE: Identification of a bacterial type III effector family with G protein mimicry functions. Cell. 2006, 124: 133-145. 10.1016/j.cell.2005.10.031.
Article
CAS
PubMed
Google Scholar
Doorbar J: Molecular biology of human papillomavirus infection and cervical cancer. Clin Sci. 2006, 110: 525-541.
Article
CAS
PubMed
Google Scholar
Carducci M, Licata L, Peluso D, Castagnoli L, Cesareni G: Enriching the viral-host interactomes with interactions mediated by SH3 domains. Amino Acids. 2010, 38 (5): 1541-1547. 10.1007/s00726-009-0375-z.
Article
CAS
PubMed
Google Scholar
Lam HYK, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB: MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics. 2010, 11: 243-10.1186/1471-2105-11-243.
Article
PubMed Central
PubMed
Google Scholar
Tonikian R, Zhang Y, Boone C, Sachdev SS: Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat Protocols. 2007, 2 (6): 1368-1386. 10.1038/nprot.2007.151.
Article
CAS
PubMed
Google Scholar
Landgraf C, Panni S, Montecchi-Palazzi L, Castagnoli L, Schneider-Mergener J, Volkmer-Engert R, Cesareni G: Protein interaction networks by proteome peptide scanning. PLoS Biol. 2004, 2: e14-10.1371/journal.pbio.0020014.
Article
PubMed Central
PubMed
Google Scholar
Stiffler MA, Chen JR, Grantcharova VP, Lei Y, Fuchs D, Allen JE, Zaslavskaia LA, MacBeath G: PDZ domain binding selectivity is optimized across the mouse proteome. Science. 2007, 317 (5836): 364-369. 10.1126/science.1144592.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kaushansky A, Allen JE, Gordus A, Stiffler MA, Karp ES, Chang BH, MacBeath G: Quantifying protein-protein interactions in high throughput using protein domain microarrays. Nat Protocols. 2010, 5 (4): 773-790. 10.1038/nprot.2010.36.
Article
CAS
PubMed
Google Scholar
Hutti JE, Jarrell ET, Chang JD, Abbott DW, Storz P, Toker A, Cantley LC, Turk BE: A rapid method for determining protein kinase phosphorylation specificity. Nat Methods. 2004, 1: 27-29. 10.1038/nmeth708.
Article
CAS
PubMed
Google Scholar
Li L, Shakhnovich EI, Mirny LA: Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci USA. 2003, 100 (8): 4463-4468. 10.1073/pnas.0737647100.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, Boone C, Bader GD, Sidhu SS: A specificity map for the PDZ domain family. PLoS Biol. 2008, 6: e239-10.1371/journal.pbio.0060239.
Article
PubMed Central
PubMed
Google Scholar
Mok J, Kim PM, Lam HYK, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JLN, Sheu YJ, Sassi HE, Sopko R, Chan CSM, Virgilio CD, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE: Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal. 2010, 3: ra12-10.1126/scisignal.2000482.
Article
PubMed Central
PubMed
Google Scholar
Cesareni G, Panni S, Nardelli G, Castagnoli L: Can we infer peptide recognition specificity mediated by SH3 domains?. FEBS Lett. 2002, 513: 38-44. 10.1016/S0014-5793(01)03307-5.
Article
CAS
PubMed
Google Scholar
Beuming T, Farid R, Sherman W: High-energy water sites determine peptide binding affinity and specificity of PDZ domains. Protein Sci. 2009, 18: 1609-1619. 10.1002/pro.177.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lichtarge O, Bourne HR, Cohen FE: An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 1996, 257: 342-358. 10.1006/jmbi.1996.0167.
Article
CAS
PubMed
Google Scholar
Göbel U, Sander C, Schneider R, Valencia A: Correlated mutations and residue contacts in proteins. Proteins: Structure, Function, and Bioinformatics. 1994, 18: 309-317. 10.1002/prot.340180402.
Article
Google Scholar
Shindyalov IN, Kolchanov NA, Sander C: Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?. Protein Eng. 1994, 7 (3): 349-358. 10.1093/protein/7.3.349.
Article
CAS
PubMed
Google Scholar
Lockless SW, Ranganathan R: Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 1999, 286 (5438): 295-299. 10.1126/science.286.5438.295.
Article
CAS
PubMed
Google Scholar
Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE: Co-evolution of proteins with their interaction partners. J Mol Biol. 2000, 299: 283-293. 10.1006/jmbi.2000.3732.
Article
CAS
PubMed
Google Scholar
Pazos F, Valencia A: In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins: Structure, Function, and Bioinformatics. 2002, 47: 219-227. 10.1002/prot.10074.
Article
CAS
Google Scholar
Ramani AK, Marcotte EM: Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol. 2003, 327: 273-284. 10.1016/S0022-2836(03)00114-1.
Article
CAS
PubMed
Google Scholar
Pazos F, Ranea JAG, Juan D, Sternberg MJE: Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol. 2005, 352 (4): 1002-1015. 10.1016/j.jmb.2005.07.005.
Article
CAS
PubMed
Google Scholar
Tiller ERM, Biro L, Li G, Tillo D: Codep: maximizing co-evolutionary interdependencies to disvoer interacting proteins. Proteins: Structure, Function, and Bioinformatics. 2006, 63 (4): 822-831. 10.1002/prot.20948.
Article
Google Scholar
Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R: Evolutionary information for specifying a protein fold. Nature. 2005, 437 (7058): 512-518. 10.1038/nature03991.
Article
CAS
PubMed
Google Scholar
Gloor GB, Martin LC, Wahl LM, Dunn SD: Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry. 2005, 44 (19): 7156-7165. 10.1021/bi050293e.
Article
CAS
PubMed
Google Scholar
Fuchs A, Martin-Galiano AJ, Kalman M, Fleishman S, Ben-Tal N, Frishman D: Co-evolving residues in membrane proteins. Bioinformatics. 2007, 23 (24): 3312-3319. 10.1093/bioinformatics/btm515.
Article
CAS
PubMed
Google Scholar
Halperin I, Wolfson H, Nussinov R: Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins: Structure, Function, and Bioinformatics. 2006, 63: 832-845. 10.1002/prot.20933.
Article
CAS
Google Scholar
Pazos F, Helmer-Citterich M, Ausiello G, Valencia A: Correlated mutations contain information about protein-protein interaction. J Mol Biol. 1997, 271: 511-523. 10.1006/jmbi.1997.1198.
Article
CAS
PubMed
Google Scholar
Shulman AI, Larson C, Mangelsdorf DJ, Ranganathan R: Structural determinants of allosteric ligand activation in RXR heterodimers. Cell. 2004, 116: 417-429. 10.1016/S0092-8674(04)00119-9.
Article
CAS
PubMed
Google Scholar
Pollock DD, Taylor WR, Goldman N: Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol. 1999, 287: 187-198. 10.1006/jmbi.1998.2601.
Article
CAS
PubMed
Google Scholar
Dekker JP, Fodor A, Aldrich RW, Yellen G: A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics. 2004, 20 (10): 1565-1572. 10.1093/bioinformatics/bth128.
Article
CAS
PubMed
Google Scholar
Martin LC, Gloor GB, Dunn SD, Wahl LM: Using information theory to search for co-evolving residues in proteins. Bioinformatics. 2005, 21 (22): 4116-4124. 10.1093/bioinformatics/bti671.
Article
CAS
PubMed
Google Scholar
Larson SM, Nardo AAD, Davidson AR: Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol. 2000, 303: 433-4446. 10.1006/jmbi.2000.4146.
Article
CAS
PubMed
Google Scholar
Galitsky B: Revealing the set of mutually correlated positions for the protein families of immunoglobulin fold. In Silico Biol. 2003, 3 (0022):
Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R: Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics. 2005, 21 (Suppl. 1): i126-i135.
Article
CAS
PubMed
Google Scholar
Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C: Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 2009, 7: 21000218-
Article
Google Scholar
Yip KY, Patel P, Kim PM, Engelman DM, McDermott D, Gerstein M: An integrated system for studying residue coevolution in proteins. Bioinformatics. 2008, 24 (2): 290-292. 10.1093/bioinformatics/btm584.
Article
CAS
PubMed
Google Scholar
Halabi N, Rivoire O, Leibler S, Ranganathan R: Protein sectors: evolutionary units of three-dimensional structure. Cell. 2009, 138: 774-786. 10.1016/j.cell.2009.07.038.
Article
PubMed Central
CAS
PubMed
Google Scholar
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T: Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA. 2009, 106: 67-72. 10.1073/pnas.0805923106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Burger L, van Nimwegen E: Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol. 2010, 6: e1000633-10.1371/journal.pcbi.1000633.
Article
PubMed Central
PubMed
Google Scholar
Cover TM, Thomas JA: Elements of Information Theory. 2006, New York: Wiley-Interscience, 2
Google Scholar
Gerstein M, Sonnhammer ELL, Chothia C: Volume changes in protein evolution. J Mol Biol. 1994, 236: 1067-1078. 10.1016/0022-2836(94)90012-4.
Article
CAS
PubMed
Google Scholar
Press WH, Flannery BP, Teukolsky SA, Vetterling WT: Numerical Recipes: The Art of Scientific Computing. 1986, Cambridge: Cambridge University Press
Google Scholar
Goebel B, Dawy Z, Hagenauer J, Mueller JC: An approximation to the distribution of finite sample size mutual information estimates. Proceedings of IEEE International Conference on Communications (ICC'05), Volume 2. 2005, 1102-1106.
Google Scholar
Aktulga HM, Kontoyiannis I, Lyznik LA, Szpankowski L, Grama AY, Szpankowski W: Identifying statistical dependence in genomic sequence via mutual information estimates. EURASIP J Bioinformatics Syst Biol. 2007, 2007: 14741-
Google Scholar
Pirovano W, Feenstra KA, Heringa J: Sequence comparison by sequence harmony identifies subtype-specific functional sites. Nucleic Acids Res. 2006, 34 (22): 6540-6548. 10.1093/nar/gkl901.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH: The WEKA data mining software: an update. SIGKDD Explorations. 2009, 11: 10-18. 10.1145/1656274.1656278.
Article
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignmnet through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22 (22): 4673-4680. 10.1093/nar/22.22.4673.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kau F, Wilczynski B, de Hoon MJL: Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009, 25 (11): 1422-1423. 10.1093/bioinformatics/btp163.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen JR, Chang BH, Allen JE, Stiffler MA, MacBeath G: Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol. 2008, 26 (9): 1041-1045. 10.1038/nbt.1489.
Article
PubMed Central
CAS
PubMed
Google Scholar
Appleton BA, Zhang Y, Wu P, Yin JP, Hunziker W, Skelton NJ, Sidhu SS, Wiesmann C: Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity. J Biol Chem. 2006, 281 (31): 22312-22320. 10.1074/jbc.M602901200.
Article
CAS
PubMed
Google Scholar
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucleic Acids Res. 2000, 28:
Google Scholar
Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS: Rapid evolution of functional complexity in a domain family. Sci Signal. 2009, 2: ra40-10.1126/scisignal.2000350.
Article
Google Scholar
Tong AHY, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CWV, Fields S, Boone C, Cesareni G: A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 2002, 295 (5553): 321-324. 10.1126/science.1064987.
Article
CAS
PubMed
Google Scholar
Douangamath A, Filipp FV, Klein AT, Barnett P, Zou P, Voorn-Brouwer T, Vega M, Mayans OM, Sattler M, Distel B, Wilmanns M: Topography for independent binding of α-helical and PPII-helical ligands to a peroxisomal SH3 domain. Mol Cell. 2002, 10: 1007-1017. 10.1016/S1097-2765(02)00749-9.
Article
CAS
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797. 10.1093/nar/gkh340.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zheng J, Trafny EA, Knighton DR, Xuong NH, Taylor SS, Eyck LFT, Sowadski JM: A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor. Acta Crystallogr D. 1993, 49: 362-365. 10.1107/S0907444993000423.
Article
CAS
PubMed
Google Scholar
Fisher RA: On the 'probable error' of a coefficient of correlation deduced from a small sample. Metron. 1921, 1: 3-32.
Google Scholar
Humphrey W, Dalke A, Schulten K: VMD: visual molecular dynamics. J Mol Graph. 1996, 14: 33-38. 10.1016/0263-7855(96)00018-5.
Article
CAS
PubMed
Google Scholar
Im YJ, Lee JH, Park SH, Park SJ, Rho SH, Kang GB, Kim E, Eom SH: Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization. J Biol Chem. 2003, 278 (48): 48099-48104. 10.1074/jbc.M306919200.
Article
CAS
PubMed
Google Scholar
Espanel X, Sudol M: Yes-associated protein and p53-binding protein-2 interact through their WW and SH3 domains. J Biol Chem. 2001, 276 (17): 14514-14523.
CAS
PubMed
Google Scholar
Musacchio A, Saraste M, Wilmanns M: High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Nat Struct Mol Biol. 1994, 1 (8): 546-551. 10.1038/nsb0894-546.
Article
CAS
Google Scholar
Yu H, Chen JK, Feng S, Dalgarno DC, Brauer AW, Schrelber SL: Structural basis for the binding of proline-rich peptides to SH3 domains. Cell. 1994, 76: 933-945. 10.1016/0092-8674(94)90367-0.
Article
CAS
PubMed
Google Scholar
Smith CM, Radzio-Andzelm E, Akamine P, Taylor SS: The catalytic subunit of cAMP-dependent protein kinase: prototype for an extended network of communication. Prog Biophys Mol Biol. 1999, 71: 313-341. 10.1016/S0079-6107(98)00059-5.
Article
CAS
PubMed
Google Scholar
Johnson DA, Akamine P, Radzio-Andzelm E, Taylor SS: Dynamics of cAMP-dependent protein kinase. Chem Rev. 2001, 101 (8): 2243-2270. 10.1021/cr000226k.
Article
CAS
PubMed
Google Scholar
Xu F, Du P, Shen H, Hu H, Wu Q, Xie J, Yu L: Correlated mutation analysis on the catalytic domains of serine/threonine protein kinases. PLoS One. 2009, 4: e5913-10.1371/journal.pone.0005913.
Article
PubMed Central
PubMed
Google Scholar
Gfeller D, Butty F, Wierzbicka M, Verschueren E, Vanhee P, Huang H, Ernst A, Dar N, Stagljar I, Serrano L, Sidhu SS, Bader GD, Kim PM: The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol. 2011, 7: 484-
Article
PubMed Central
PubMed
Google Scholar
DREAM4, Challenge 1: Peptide Recognition Domain (PRD) Specificity Prediction. 2009, [http://wiki.c2b2.columbia.edu/dream/index.php/D4c1]
London N, Movshovitz-Attias D, Schueler-Furman O: The structural basis of peptide-protein binding strategies. Structure. 2010, 18: 188-199. 10.1016/j.str.2009.11.012.
Article
CAS
PubMed
Google Scholar