Abstract
By using a mixture model for the density distribution of the three pseudobond angles formed by C α atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural alphabet. This coarse-graining procedure converts a 3D structure to a 1D code sequence. A substitution matrix between these letters is constructed based on the structural alignments of the FSSP database.
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References
Asai, K., Hazamizu, S., Handa, K.: Secondary structure prediction by hidden Markov model. CABIOS 9, 141-146 (1993)
Burge, C., Karlin, S.: Prediction of complete gene structures in human genomic DNA. J. Mol. Evol. 268, 78–94 (1997)
Bystroff, C., Baker, D.: Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol. 281, 565–577 (1998)
Camproux, A.C., Tuffery, P., Chevrolat, J.P., Boisvieux, J.F., Hazout, S.: Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng. 12, 1063–1073 (1999)
Edgoose, T., Allison, L., Dowe, D.L.: An MML classification of protein structure that knows about angles and sequences. In: Proc. 3rd Pacific Symposium on Biocomputing (PSB 1998), Hawaii, USA, pp. 585–596 (1998)
Fujiwara, Y., Asogawa, M., Konagaya, A.: Stochastic motif extraction using hidden Markov model. In: Proc. ISMB 1994, pp. 121–129 (1994)
Henikoff, S., Henikoff, J.G.: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915–10919 (1992)
Holm, L., Sander, C.: Touring protein fold space with Dali/FSSP. Nucleic Acids Research 26, 316–319 (1998)
Krogh, A., Brown, M., Mian, I.S., Sjölander, K., Haussler, D.: Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol. 235, 1501–1531 (1994)
Nelder, J.A., Mead, R.: A simplex method for function minimization. Computer J. 7, 308–313 (1965)
Park, B.H., Levitt, M.: The complexity and accuracy of discrete state models of protein structure, J. Mol. Biol. 249, 493–507 (1995)
Rabiner, L.R.: A tutorial on hidden Markov model and selected applications in speech recognition. Proc. IEEE 77, 257–285 (1989)
Rooman, M.J., Kocher, J.-P.A., Wodak, S.J.: Prediction of protein backbone conformation based on seven structure assignments: Influnce of local interacti1ons. J. Mol. Biol. 221, 961–979 (1991)
Zheng, W.M.: Clustering of amino acids for protein secondary structure prediction. J. Bioinfor. Comp. Biol. 2, 333–342 (2004)
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Zheng, WM., Liu, X. (2005). A Protein Structural Alphabet and Its Substitution Matrix CLESUM. In: Priami, C., Zelikovsky, A. (eds) Transactions on Computational Systems Biology II. Lecture Notes in Computer Science(), vol 3680. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11567752_4
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DOI: https://doi.org/10.1007/11567752_4
Publisher Name: Springer, Berlin, Heidelberg
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