By H. Cabannes, M. Holt, V. V. Rusanov
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34 1. Amino acid composition (AA): This basic feature enables us to capture the global information of a TM helix. Each residue of a peptide is represented by a vector of length of 20 which is indicated by 1 in the position corresponding to the amino acid type of the residue, and 0 otherwise. 2. Di-peptide composition (DP): We consider the coupling effect of two adjacent residues that contain global information along the sequence. This feature is represented by the pair-residue occurrence probability, P(X,Y) where (X,Y) is an ordered pair of amino acids of X followed by Y.
P. Tuffery, F. Guyon, and P. Derreumaux. Improved greedy algorithm for protein structure reconstruction. Journal of Computational Chemistry, 26:506513, 2005. 21. G. Wang and R. L. Dunbrack JR. Scoring profileto-profile sequence alignments. Protein Science, 13:1612-1626, 2004. tw Motivation: A key class of membrane proteins contains one or more transmembrane (TM) helices, traversing the membrane lipid bilayer. Various properties such as the length, arrangement and topology or orientation of TM helices, are closely related to a protein's functions.
J. Chandonia, G. Hon, N. S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S. E. Brenner. The astral compendium in 2004. Nucleic Acids Research, 2004. 4. M. M. Mattheyses. A linear-time heuristic for improving network partitions. Proceedings of the 19th Design Automation Conference, 1982. 5. A. Heger and L. Holm. Picasso: generating a covering set of protein family profiles. Bioinformatics, 2001. 6. S. Henikoff and J. G. HenikofT. Amino acid subsitution matrices from protein blocks. PNAS, 89:1091510919, 1992.
6th Int'l Conference on Numerical Methods in Fluid Dynamics by H. Cabannes, M. Holt, V. V. Rusanov
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