Abstract
Protein structure prediction is one of the main challenges in Bioinformatics. An useful representation for protein 3D structure is the protein contact map. In this work, we propose an evolutionary approach for contact map prediction based on amino acids physicochemical properties. The evolutionary algorithm produces a set of rules that identifies contacts between amino acids. The rules obtained by the algorithm imposes a set of conditions on four amino acid properties in order to predict contacts. Results obtained confirm the validity of the proposal.
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References
Anfinsen, C.: The formation and stabilization of protein structure. Biochem. J. 128, 737–749 (1972)
Zhang, Y.: I-tasser: fully automated protein structure prediction in casp8. Proteins: Structure, Function, and Bioinformatics 77, 100–113 (2009)
Tegge, A., Wang, Z., Eickholt, J., Cheng, J.: Nncon: Improved protein contact map prediction using 2d-recursive neural networks. Nucleic Acids Research 37(2), 515–518 (2009)
Gupta, N., Mangal, N., Biswas, S.: Evolution and similarity evaluation of protein structures in contact map space. Proteins: Structure, Function, and Bioinformatics 59, 196–204 (2005)
Unger, R., Moult, J.: Genetic algorithms for protein folding simulations. Biochim. Biophys. 231, 75–81 (1993)
Cui, Y., Chen, R.S., Hung, W.: Protein folding simulation with genetic algorithm and supersecondary structure constraints. Proteins: Structure, Function and Genetics 31, 247–257 (1998)
Zhang, G., Han, K.: Hepatitis c virus contact map prediction based on binary strategy. Comp. Biol. and Chem. 31, 233–238 (2007)
Protein data bank web, http://www.pdb.org
Gu, J., Bourne, P.E.: Structural Bioinformatics (Methods of Biochemical Analysis). Wiley-Blackwell, Chichester (2003)
Kyte, J., Doolittle, R.F.: A simple method for displaying the hydropathic character of a protein. J. J. Mol. Bio. 157, 105–132 (1982)
Grantham, R.: Amino acid difference formula to help explain protein evolution. J. J. Mol. Bio. 185, 862–864 (1974)
Klein, P., Kanehisa, M., DeLisi, C.: Prediction of protein function from sequence properties: Discriminant analysis of a data base. Biochim. Biophys. 787, 221–226 (1984)
Dawson, D.M.: The Biochemical Genetics of Man. In: Brock, D.J.H., Mayo, O. (eds.) (1972)
Fariselli, P., Olmea, O., Valencia, A., Casadio, R.: Prediction of contact map with neural networks and correlated mutations. Protein Engineering 14, 133–154 (2001)
Zhang, G.Z., Huang, D.S., Quan, Z.H.: Combining a binary input encoding scheme with rbfnn for globulin protein inter-residue contact map prediction. Pattern Recognition Letters 16(10), 1543–1553 (2005)
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Chamorro, A.E.M., Divina, F., Aguilar-Ruiz, J.S. (2011). Evolutionary Protein Contact Maps Prediction Based on Amino Acid Properties. In: Corchado, E., Kurzyński, M., Woźniak, M. (eds) Hybrid Artificial Intelligent Systems. HAIS 2011. Lecture Notes in Computer Science(), vol 6679. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21222-2_37
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DOI: https://doi.org/10.1007/978-3-642-21222-2_37
Publisher Name: Springer, Berlin, Heidelberg
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