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For: Ofran Y, Rost B. ISIS: interaction sites identified from sequence. Bioinformatics 2007;23:e13-6. [PMID: 17237081 DOI: 10.1093/bioinformatics/btl303] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
101
Munteanu CR, Pimenta AC, Fernandez-Lozano C, Melo A, Cordeiro MNDS, Moreira IS. Solvent accessible surface area-based hot-spot detection methods for protein-protein and protein-nucleic acid interfaces. J Chem Inf Model 2015;55:1077-86. [PMID: 25845030 DOI: 10.1021/ci500760m] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
102
Maheshwari S, Brylinski M. Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 2015;16:1025-34. [PMID: 25797794 DOI: 10.1093/bib/bbv009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 01/20/2023]  Open
103
Wierschin T, Wang K, Welter M, Waack S, Stanke M. Combining features in a graphical model to predict protein binding sites. Proteins 2015;83:844-52. [PMID: 25663045 DOI: 10.1002/prot.24775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 01/16/2015] [Accepted: 01/26/2015] [Indexed: 11/08/2022]
104
Wiech EM, Cheng HP, Singh SM. Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. Protein Sci 2015;24:319-27. [PMID: 25492513 PMCID: PMC4353358 DOI: 10.1002/pro.2616] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 12/12/2022]
105
Aumentado-Armstrong TT, Istrate B, Murgita RA. Algorithmic approaches to protein-protein interaction site prediction. Algorithms Mol Biol 2015;10:7. [PMID: 25713596 PMCID: PMC4338852 DOI: 10.1186/s13015-015-0033-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 01/07/2015] [Indexed: 12/19/2022]  Open
106
Ntostis P, Agiannitopoulos K, Tsaousis G, Pantos K, Lamnissou K. Evidence for association of the rs605059 polymorphism of HSD17B1 gene with recurrent spontaneous abortions. J Matern Fetal Neonatal Med 2014;28:2250-3. [PMID: 25394609 DOI: 10.3109/14767058.2014.984289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
107
Yugandhar K, Gromiha MM. Protein–protein binding affinity prediction from amino acid sequence. Bioinformatics 2014;30:3583-9. [DOI: 10.1093/bioinformatics/btu580] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
108
Dong Z, Wang K, Dang TKL, Gültas M, Welter M, Wierschin T, Stanke M, Waack S. CRF-based models of protein surfaces improve protein-protein interaction site predictions. BMC Bioinformatics 2014;15:277. [PMID: 25124108 PMCID: PMC4150965 DOI: 10.1186/1471-2105-15-277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 08/01/2014] [Indexed: 11/13/2022]  Open
109
Andreani J, Guerois R. Evolution of protein interactions: From interactomes to interfaces. Arch Biochem Biophys 2014;554:65-75. [DOI: 10.1016/j.abb.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/28/2014] [Accepted: 05/12/2014] [Indexed: 12/16/2022]
110
Esmaielbeiki R, Nebel JC. Scoring docking conformations using predicted protein interfaces. BMC Bioinformatics 2014;15:171. [PMID: 24906633 PMCID: PMC4057934 DOI: 10.1186/1471-2105-15-171] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 05/29/2014] [Indexed: 12/22/2022]  Open
111
Villoutreix BO, Kuenemann MA, Poyet JL, Bruzzoni-Giovanelli H, Labbé C, Lagorce D, Sperandio O, Miteva MA. Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform 2014;33:414-437. [PMID: 25254076 PMCID: PMC4160817 DOI: 10.1002/minf.201400040] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
112
Lua RC, Marciano DC, Katsonis P, Adikesavan AK, Wilkins AD, Lichtarge O. Prediction and redesign of protein-protein interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014;116:194-202. [PMID: 24878423 DOI: 10.1016/j.pbiomolbio.2014.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/02/2014] [Accepted: 05/17/2014] [Indexed: 12/14/2022]
113
Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res 2014;42:W337-43. [PMID: 24799431 PMCID: PMC4086098 DOI: 10.1093/nar/gku366] [Citation(s) in RCA: 443] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
114
Dhole K, Singh G, Pai PP, Mondal S. Sequence-based prediction of protein–protein interaction sites with L1-logreg classifier. J Theor Biol 2014;348:47-54. [DOI: 10.1016/j.jtbi.2014.01.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 01/10/2014] [Accepted: 01/22/2014] [Indexed: 11/30/2022]
115
Wang B, Huang DS, Jiang C. A new strategy for protein interface identification using manifold learning method. IEEE Trans Nanobioscience 2014;13:118-23. [PMID: 24771594 DOI: 10.1109/tnb.2014.2316997] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
116
Yugandhar K, Gromiha MM. Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches. Proteins 2014;82:2088-96. [PMID: 24648146 DOI: 10.1002/prot.24564] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/14/2014] [Indexed: 12/16/2022]
117
Falero A, Marrero K, Trigueros S, Fando R. Characterization of the RstB2 protein, the DNA-binding protein of CTXϕ phage from Vibrio cholerae. Virus Genes 2014;48:518-27. [PMID: 24643345 DOI: 10.1007/s11262-014-1053-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/28/2014] [Indexed: 11/25/2022]
118
Feiglin A, Ashkenazi S, Schlessinger A, Rost B, Ofran Y. Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence. MOLECULAR BIOSYSTEMS 2014;10:787-94. [PMID: 24457447 DOI: 10.1039/c3mb70411d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
119
Shen HB, Yi DL, Yao LX, Yang J, Chou KC. Knowledge-based computational intelligence development for predicting protein secondary structures from sequences. Expert Rev Proteomics 2014;5:653-62. [DOI: 10.1586/14789450.5.5.653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
120
CompASM: an Amber-VMD alanine scanning mutagenesis plug-in. MARCO ANTONIO CHAER NASCIMENTO 2014. [DOI: 10.1007/978-3-642-41163-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
121
Bhaskara RM, Padhi A, Srinivasan N. Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling. Proteins 2013;82:1219-34. [PMID: 24375512 DOI: 10.1002/prot.24486] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 11/04/2013] [Accepted: 11/19/2013] [Indexed: 01/08/2023]
122
Agrawal NJ, Helk B, Trout BL. A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein. FEBS Lett 2013;588:326-33. [PMID: 24239538 DOI: 10.1016/j.febslet.2013.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 11/29/2022]
123
An accurate method for prediction of protein-ligand binding site on protein surface using SVM and statistical depth function. BIOMED RESEARCH INTERNATIONAL 2013;2013:409658. [PMID: 24195070 PMCID: PMC3806129 DOI: 10.1155/2013/409658] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/15/2013] [Accepted: 08/29/2013] [Indexed: 11/17/2022]
124
Ozbek P, Soner S, Haliloglu T. Hot spots in a network of functional sites. PLoS One 2013;8:e74320. [PMID: 24023934 PMCID: PMC3759471 DOI: 10.1371/journal.pone.0074320] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 08/02/2013] [Indexed: 12/05/2022]  Open
125
Cloud prediction of protein structure and function with PredictProtein for Debian. BIOMED RESEARCH INTERNATIONAL 2013;2013:398968. [PMID: 23971032 PMCID: PMC3732596 DOI: 10.1155/2013/398968] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 07/05/2013] [Indexed: 11/18/2022]
126
Wang L, Hou Y, Quan H, Xu W, Bao Y, Li Y, Fu Y, Zou S. A compound-based computational approach for the accurate determination of hot spots. Protein Sci 2013;22:1060-70. [PMID: 23776011 DOI: 10.1002/pro.2296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/27/2013] [Accepted: 06/01/2013] [Indexed: 12/21/2022]
127
Andreani J, Faure G, Guerois R. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. ACTA ACUST UNITED AC 2013;29:1742-9. [PMID: 23652426 DOI: 10.1093/bioinformatics/btt260] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
128
Andorf CM, Honavar V, Sen TZ. Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PLoS One 2013;8:e56833. [PMID: 23431393 PMCID: PMC3576370 DOI: 10.1371/journal.pone.0056833] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/16/2013] [Indexed: 02/01/2023]  Open
129
Ribeiro JV, Cerqueira NMFSA, Moreira IS, Fernandes PA, Ramos MJ. CompASM: an Amber-VMD alanine scanning mutagenesis plug-in. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1271-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
130
Li BQ, Feng KY, Chen L, Huang T, Cai YD. Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFS. PLoS One 2012;7:e43927. [PMID: 22937126 PMCID: PMC3429425 DOI: 10.1371/journal.pone.0043927] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/26/2012] [Indexed: 11/19/2022]  Open
131
Hamp T, Rost B. Alternative protein-protein interfaces are frequent exceptions. PLoS Comput Biol 2012;8:e1002623. [PMID: 22876170 PMCID: PMC3410849 DOI: 10.1371/journal.pcbi.1002623] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 06/11/2012] [Indexed: 11/18/2022]  Open
132
Chen P, Wong L, Li J. Detection of outlier residues for improving interface prediction in protein heterocomplexes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012;9:1155-1165. [PMID: 22529331 DOI: 10.1109/tcbb.2012.58] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
133
Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. BMC Genomics 2012;13 Suppl 4:S11. [PMID: 22759649 PMCID: PMC3394413 DOI: 10.1186/1471-2164-13-s4-s11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
134
Schaefer C, Rost B. Predict impact of single amino acid change upon protein structure. BMC Genomics 2012;13 Suppl 4:S4. [PMID: 22759652 PMCID: PMC3395892 DOI: 10.1186/1471-2164-13-s4-s4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
135
Chen CT, Peng HP, Jian JW, Tsai KC, Chang JY, Yang EW, Chen JB, Ho SY, Hsu WL, Yang AS. Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. PLoS One 2012;7:e37706. [PMID: 22701576 PMCID: PMC3368894 DOI: 10.1371/journal.pone.0037706] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 04/23/2012] [Indexed: 11/18/2022]  Open
136
Feng ZP, Chandrashekaran IR, Low A, Speed TP, Nicholson SE, Norton RS. The N-terminal domains of SOCS proteins: a conserved region in the disordered N-termini of SOCS4 and 5. Proteins 2012;80:946-57. [PMID: 22423360 DOI: 10.1002/prot.23252] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
137
Garcia-Garcia J, Bonet J, Guney E, Fornes O, Planas J, Oliva B. Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details. Mol Inform 2012;31:342-62. [PMID: 27477264 DOI: 10.1002/minf.201200005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 03/09/2012] [Indexed: 11/08/2022]
138
Dakshinamoorthy G, Samykutty AK, Munirathinam G, Shinde GB, Nutman T, Reddy MV, Kalyanasundaram R. Biochemical characterization and evaluation of a Brugia malayi small heat shock protein as a vaccine against lymphatic filariasis. PLoS One 2012;7:e34077. [PMID: 22496777 PMCID: PMC3320633 DOI: 10.1371/journal.pone.0034077] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/21/2012] [Indexed: 12/15/2022]  Open
139
Qi Y, Oja M, Weston J, Noble WS. A unified multitask architecture for predicting local protein properties. PLoS One 2012;7:e32235. [PMID: 22461885 PMCID: PMC3312883 DOI: 10.1371/journal.pone.0032235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 01/25/2012] [Indexed: 01/27/2023]  Open
140
Jordan RA, EL-Manzalawy Y, Dobbs D, Honavar V. Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics 2012;13:41. [PMID: 22424103 PMCID: PMC3386866 DOI: 10.1186/1471-2105-13-41] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 03/18/2012] [Indexed: 11/10/2022]  Open
141
Druggability assessment of protein-protein interfaces. Future Med Chem 2012;3:2021-38. [PMID: 22098351 DOI: 10.4155/fmc.11.156] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
142
Partner-aware prediction of interacting residues in protein-protein complexes from sequence data. PLoS One 2011;6:e29104. [PMID: 22194998 PMCID: PMC3237601 DOI: 10.1371/journal.pone.0029104] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 11/21/2011] [Indexed: 12/22/2022]  Open
143
Zellner H, Staudigel M, Trenner T, Bittkowski M, Wolowski V, Icking C, Merkl R. Prescont: Predicting protein-protein interfaces utilizing four residue properties. Proteins 2011;80:154-68. [DOI: 10.1002/prot.23172] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 08/18/2011] [Accepted: 08/29/2011] [Indexed: 12/26/2022]
144
Qiu Z, Wang X. Prediction of protein-protein interaction sites using patch-based residue characterization. J Theor Biol 2011;293:143-50. [PMID: 22037062 DOI: 10.1016/j.jtbi.2011.10.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 09/13/2011] [Accepted: 10/15/2011] [Indexed: 10/15/2022]
145
Gromiha MM, Saranya N, Selvaraj S, Jayaram B, Fukui K. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes. Proteome Sci 2011;9 Suppl 1:S13. [PMID: 22166143 PMCID: PMC3289074 DOI: 10.1186/1477-5956-9-s1-s13] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
146
Sahu SS, Panda G. Efficient localization of hot spots in proteins using a novel S-transform based filtering approach. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:1235-1246. [PMID: 21778522 DOI: 10.1109/tcbb.2010.109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
147
Chen R, Chen W, Yang S, Wu D, Wang Y, Tian Y, Shi Y. Rigorous assessment and integration of the sequence and structure based features to predict hot spots. BMC Bioinformatics 2011;12:311. [PMID: 21798070 PMCID: PMC3176265 DOI: 10.1186/1471-2105-12-311] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 07/29/2011] [Indexed: 12/02/2022]  Open
148
Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef. PLoS One 2011;6:e20735. [PMID: 21738584 PMCID: PMC3125164 DOI: 10.1371/journal.pone.0020735] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 05/08/2011] [Indexed: 01/03/2023]  Open
149
Xue LC, Dobbs D, Honavar V. HomPPI: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics 2011;12:244. [PMID: 21682895 PMCID: PMC3213298 DOI: 10.1186/1471-2105-12-244] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 06/17/2011] [Indexed: 01/12/2023]  Open
150
Falero A, Caballero A, Trigueros S, Pérez C, Campos J, Marrero K, Fando R. Characterization of the single-stranded DNA binding protein pV(VGJΦ) of VGJΦ phage from Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA 2011;1814:1107-12. [PMID: 21586349 DOI: 10.1016/j.bbapap.2011.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 03/22/2011] [Accepted: 04/21/2011] [Indexed: 01/01/2023]
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