Summary
Inter-residue contacts map prediction is one of the most important intermediate steps to the protein folding problem. In this paper, we focus on the problem of protein inter-residue contacts map prediction based on neural network technique. Firstly, we use a genetic algorithm (GA) to optimize the radial basis function widths and hidden centers of a radial basis function neural network (RBFNN), then a novel binary encoding scheme is employed to train the network for the purpose of learning and predicting the inter-residue contacts patterns of protein sequences got from the protein data bank (PDB). The experimental evidence indicates the utility of our proposed encoding strategy and GA optimized RBFNN. Moreover, the simulation results demonstrate that the network got a better performance for these proteins, whose residue length falls into the area of (100, 300), and the predicted accuracy with a contact threshold of 7 Å scores higher than the other 3 values with 5, 6, and 8 Å .
Similar content being viewed by others
References
K. Park M. Vendruscolo E. Domany (2000) ArticleTitleProteins Struct Funct. Genet. 40 237 Occurrence Handle1:CAS:528:DC%2BD3cXkt1ahtro%3D
M. Vendruscolo R. Najmanovich E. Domany (2000) ArticleTitleProteins Struct Funct. Genet. 38 134 Occurrence Handle1:CAS:528:DC%2BD3cXks1Gmtg%3D%3D
P. Fariselli O. Olmea A. Valencia R. Casadio (2001) Protein Eng. 14 IssueID11 835 Occurrence Handle10.1093/protein/14.11.835 Occurrence Handle1:CAS:528:DC%2BD38XjtVentA%3D%3D Occurrence Handle11742102
Hamilton, M., Burrage, K., Raga, M.A., Hubor, T., Protein contact prediction using patterns of correlation, http://foo.maths.uq.edu.au/˜nick/Protein/Dataset/protein contact.pdf
Hu, J., Shen, X., Shao, Y., Bystroff, C., Zaki, M. J., Mining Protein Contact Maps, http://www.cs.rpi.edu/˜zaki/BIOKDD02/02-hu.pdf
M.S. Singer G. Vriend R.P. Bywater (2002) Protein Eng. 15 IssueID9 721 Occurrence Handle10.1093/protein/15.9.721 Occurrence Handle1:CAS:528:DC%2BD38XptlOhtLY%3D Occurrence Handle12456870
S. Fairchild R. Pachter R. Perrin (1997) Math J. 5 IssueID4 64
A.J. Ketterman P. Prommeenate C. Boonchauy U. Chanama S. Leetachewa N. Plomtet L. Prapanthadasa (2001) Biochem. Mol. Biol. 31 65 Occurrence Handle10.1016/S0965-1748(00)00106-5 Occurrence Handle1:CAS:528:DC%2BD3cXotlCgtLw%3D
Zhang, G.Z., Huang, D.S., Wang, H.Q., In the Proceedings of the 2004 International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Montrġl, QuĢec, Canada, May 17–21, 2004, pp. V573–576
Zhang, G.-Z., Huang, D.S., In the Proceedings of the 2004 IEEE Congress on Evolutionary Computation, Portland, Oregon, Vol. 1, June 19–23, 2004, pp. 1015–1019
E.L.L. Sonnhammer J.C. Wootton (1998) ArticleTitleJ. Mol Graph. Model 16 1 Occurrence Handle10.1016/S1093-3263(98)00009-6 Occurrence Handle1:CAS:528:DyaK1cXmsVynurw%3D
L. Mirny E. Domany (1996) Proteins 26 319 Occurrence Handle10.1002/(SICI)1097-0134(199612)26:4<391::AID-PROT3>3.0.CO;2-F
P. Fariselli O. Olmea A. Valencia R. Casadio (2001) Proteins (Suppl)5 157 Occurrence Handle10.1002/prot.1173
P. Fariselli R. Casadio (1999) Protein Eng 12 15 Occurrence Handle10.1093/protein/12.1.15 Occurrence Handle1:CAS:528:DyaK1MXht1Kgsrk%3D Occurrence Handle10065706
Z.O. Wang T. Zhu (2000) Neural Networks 13 545 Occurrence Handle10.1016/S0893-6080(00)00029-0 Occurrence Handle1:STN:280:DC%2BD3M%2FkvVGhtQ%3D%3D Occurrence Handle10946399
C.A. Orengo A.D. Michie S. Jones D.T. Jones M.B. Swindells J.M. Thornton (1997) Structure 5 IssueID8 1093 Occurrence Handle10.1016/S0969-2126(97)00260-8 Occurrence Handle1:CAS:528:DyaK2sXmt1Wgs74%3D Occurrence Handle9309224
Belloir, F., Fache, A., Billat, A. In the Proceedings of the European Symposiun on Artificial Neural Networks, Bruges (Belgium), D-Facto publicl., ISBN 2-600049-9-X, April 21–23 1999, pp. 399–404
De Jong, K., Learning with Genetic Algorithms: An Overview, Machine Learning Vol. 3, Kluwer Academic Publishers, 1998
S.-B. Cho (1999) Fuzzy Sets Syst. 103 339 Occurrence Handle10.1016/S0165-0114(98)00232-2
L. Guo D.S. Huang W. Zhao (2003) IEE Electronics Lett. 39 IssueID22 1600 Occurrence Handle10.1049/el:20031021
Guo, L., Huang, D.S., Zhao W.-B., In the Proceedings of the International Joint Conference on Neural Networks (IJCNN2003), Portland, Oregon, July 20–24, 2003, pp. 3213–3217
Zhang G.-Z. Huang D.S. (2004) The 2004 International Joint Conference on Neural Networks (IJCNN2004) Budapest Hungary 25–29
H.M. Berman J. Westbrook Z. Feng G. Gilliland T.N. Bhat Weissig H. Shindyalov I.N. P.E. Bourne (2000) Nucleic Acids Res. 28 235 Occurrence Handle10.1093/nar/28.1.235 Occurrence Handle1:CAS:528:DC%2BD3cXhvVKjt7w%3D Occurrence Handle10592235
W. Kabsch C. Sander (1983) Biopolymers 2577 22
J. Guo H. Chen Z. Sun Y. Lin (2004) ArticleTitleProteins Struct Funct. Bioinform. 54 738 Occurrence Handle10.1002/prot.10634 Occurrence Handle1:CAS:528:DC%2BD2cXitVGgur8%3D
G. Benedetti S. Morosetti (1995) Biophys Chem 55 253 Occurrence Handle10.1016/0301-4622(94)00130-C Occurrence Handle1:CAS:528:DyaK2MXmsFGnurc%3D Occurrence Handle7542936
H. Yu W. Liang (2001) ArticleTitleComput Indus. Eng. 39 337 Occurrence Handle10.1016/S0360-8352(01)00010-9
D.S. Huang S.D. Ma (1999) J. Intel Syst 9 IssueID1 1
F.M.G. Pearl D. Lee J.E. Bray I. Sillitoe A.E. Todd A.P. Harrison J.M. Thornton C.A. Orengo (2000) Nucleic Acids Res 28 IssueID1 277 Occurrence Handle10.1093/nar/28.1.277 Occurrence Handle1:CAS:528:DC%2BD3cXhvVKjtL0%3D Occurrence Handle10592246
D.S. Huang (1999) Int. J Pattern Recog. Artif. Intel. 13 IssueID6 945 Occurrence Handle10.1142/S0218001499000525
S. Sen (2003) Biophys Chem. 103 35 Occurrence Handle10.1016/S0301-4622(02)00230-2 Occurrence Handle1:CAS:528:DC%2BD38XpslSmtL4%3D Occurrence Handle12504253
T.S. Kumarevel M.M. Gromiba M.N. Ponnuswamy (2000) Biophys Chem. 88 81 Occurrence Handle10.1016/S0301-4622(00)00201-5 Occurrence Handle1:CAS:528:DC%2BD3cXotVCrs74%3D Occurrence Handle11152278
L.X. Zhang J. Li Z. Jiang A. Xia (2003) Polymer. 44 1751 Occurrence Handle10.1016/S0032-3861(03)00021-1 Occurrence Handle1:CAS:528:DC%2BD3sXhtFCmtLo%3D
M. Michael Gromiha J. Selvaraj S. (2001) Mol Biol. 310 27 Occurrence Handle10.1006/jmbi.2001.4775
M.S. Singer G. Vriend R.P. Bywter (2002) Protein Eng., 15 721
K.-H. Park J.-E. Suk R. Jacobsen W.R. Gray J.M. Mcintosh K.-H. Han (2001) J. Biol Chem. 276 IssueID52 49028 Occurrence Handle10.1074/jbc.M107798200 Occurrence Handle1:CAS:528:DC%2BD38Xktlensg%3D%3D Occurrence Handle11641403
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Zhang, GZ., Huang, DS. Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. J Comput Aided Mol Des 18, 797–810 (2004). https://doi.org/10.1007/s10822-005-0578-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10822-005-0578-7