[1]
|
Chen, C.-T., Peng, H.-P., Jian, J.-W., Tsai, K.-C., Chang, J.-Y., Yang, E.-W., Chen, J.-B., Ho, S.-Y., Hsu, W.-L. and Yang, A.-S. (2012) Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. PloS ONE, 7, e37706.
http://dx.doi.org/10.1371/journal.pone.0037706
|
[2]
|
Jordan, A.R., El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2012) Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics, 13, 41.
http://dx.doi.org/10.1186/1471-2105-13-41
|
[3]
|
Bradford, J.R. and Westhead, D.R. (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics, 21, 1487-1494.
http://dx.doi.org/10.1093/bioinformatics/bti242
|
[4]
|
Zhou, H.X. and Shan, Y. (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44, 336-343.
http://dx.doi.org/10.1002/prot.1099
|
[5]
|
Burgoyne, N.J. and Jackson, R.M. (2006) Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics, 22, 1335-1342. http://dx.doi.org/10.1093/bioinformatics/btl079
|
[6]
|
Friedrich, T., Pils, B., Dandekar, T. and Muller, T. (2006) Modelling interaction sites in protein domains with interaction profile hidden Markov models. Bioinformatics, 22, 2851-2857.
http://dx.doi.org/10.1093/bioinformatics/btl486
|
[7]
|
Ofran, Y. and Rost, B. (2003) Predicted protein-protein interaction sites from local sequence information. FEBS Letters, 544, 236-239.
http://dx.doi.org/10.1016/S0014-5793(03)00456-3
|
[8]
|
Zhou, H.-X. and Qin, S. (2007) Interaction-site prediction for protein complexes: A critical assessment. Bioinformatics, 23, 2203-2209.
http://dx.doi.org/10.1093/bioinformatics/btm323
|
[9]
|
Ritchie, D.W. (2008) Recent progress and future directions in protein-protein docking. Current Protein and Peptide Science, 9, 1-15.
http://dx.doi.org/10.2174/138920308783565741
|
[10]
|
Li, B. and Kihara, D. (2012) Protein docking prediction using predicted protein-protein interface. BMC Bioinformatics, 13, 7. http://dx.doi.org/10.1186/1471-2105-13-7
|
[11]
|
Thattai, M., Burak, Y. and Shraiman, B.I. (2007) The origins of specificity in polyketide synthase protein interactions. PLoS Computational Biology, 3, 1827-1835.
http://dx.doi.org/10.1371/journal.pcbi.0030186
|
[12]
|
Burger, L. and Van Nimwegen, E. (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular Systems Biology, 4, 1-14. http://dx.doi.org/10.1038/msb4100203
|
[13]
|
White, R.A., Szurmant, H., Hoch, J.A. and Hwa, T. (2007) Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods in Enzymology, 422, 75-101.
http://dx.doi.org/10.1016/S0076-6879(06)22004-4
|
[14]
|
Weigt, M., White, R.A., Szurmant, H., Hoch, J.A. and Hwa, T. (2009) Identification of direct residue contacts in protein-protein interaction by message passing. PNAS, 106, 67-72. http://dx.doi.org/10.1073/pnas.0805923106
|
[15]
|
González, A.J., Liao, L. and Wu, C.H. (2013) Prediction of contact matrix for protein-protein interaction. Bioinformatics, 29, 1018-1025.
http://dx.doi.org/10.1093/bioinformatics/btt076
|
[16]
|
Ghoorah, A.W., Devignes, M.-D., Smaïl-Tabbone, M. and Ritchie, D.W. (2011) Spatial clustering of protein binding sites for template based protein docking. Bioinformatics, 27, 2820-2827.
http://dx.doi.org/10.1093/bioinformatics/btr493
|
[17]
|
Aloy, P., Ceulemans, H., Stark, A. and Russell, R.B. (2003) The relationship between sequence and interaction divergence in proteins. Journal of Molecular Biology, 332, 989-998.
http://dx.doi.org/10.1016/j.jmb.2003.07.006
|
[18]
|
Keskin, O. and Nussinov, R. (2007) Similar binding sites and different partners: Implications to shared proteins in cellular pathways. Structure, 15, 341-354.
http://dx.doi.org/10.1016/j.str.2007.01.007
|
[19]
|
Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D.S., Sander, C., Zecchina, R., Onuchic, J.N., Hwa, T. and Weigt, M. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences of the United States of America, 108, E1293-E1301. http://dx.doi.org/10.1073/pnas.1111471108
|
[20]
|
Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T. and Kanehisa, M. (2008) AAindex: Amino acid index database, progress report 2008. Nucleic Acids Research, 36, D202-D205.
http://dx.doi.org/10.1093/nar/gkm998
|
[21]
|
Krogh, A., Brown, M., Mian, I.S., Jokander, K. and David, H. (1994) Hidden Markov Models in Computational Biology Applications to Protein Modeling. Journal of Molecular Biology, 235, 1501-1531.
http://dx.doi.org/10.1006/jmbi.1994.1104
|
[22]
|
Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics Review, 14, 755-763.
|
[23]
|
González, A.J. and Liao, L. (2010) Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. BMC Bioinformatics, 11, 537.
http://dx.doi.org/10.1186/1471-2105-11-537
|
[24]
|
González, A.J. and Liao, L. (2009) Constrained fisher scores derived from interaction profile hidden Markov models improve protein to protein interaction. Proceedings of the First International Conference BICoB 2009, New Orleans, 8-10 April 2009, 236-247.
|
[25]
|
Hopf, T.A., Colwell, L.J., Sheridan, R., Rost, B., Sander, C. and Marks, D.S. (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell, 149, 1607-1621.
http://dx.doi.org/10.1016/j.cell.2012.04.012
|
[26]
|
Marks, D.S., Colwell, L.J., Sheridan, R., Hopf, A.T., Pagnani, A., Zecchina, R. and Sander, C. (2011) Protein 3D structure computed from evolutionary sequence variation. PloS ONE, 6, e28766.
http://dx.doi.org/10.1371/journal.pone.0028766
|
[27]
|
Procaccini, A., Lunt, B., Szurmant, H., Hwa, T. and Weigt, M. (2011) Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PloS ONE, 6, e19729.
http://dx.doi.org/10.1371/journal.pone.0019729
|
[28]
|
Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J, Heger, A., Holm, L., Sonnhammer, E.L.L., Eddy, S.R., Bateman, A. and Finn, R.D. (2012) The Pfam protein families database. Nucleic Acids Research, 40, D290-D301. http://dx.doi.org/10.1093/nar/gkr1065
|
[29]
|
Stein, A., Russell, R.B. and Aloy, P. (2005) 3did: Interacting protein domains of known three-dimensional structure. Nucleic Acids Research, 33, D413-D417.
http://dx.doi.org/10.1093/nar/gki037
|