Use of residue pairs in protein sequence-sequence and sequence-structure alignments
نویسندگان
چکیده
منابع مشابه
Use of residue pairs in protein sequence-sequence and sequence-structure alignments.
Two new sets of scoring matrices are introduced: H2 for the protein sequence comparison and T2 for the protein sequence-structure correlation. Each element of H2 or T2 measures the frequency with which a pair of amino acid types in one protein, k-residues apart in the sequence, is aligned with another pair of residues, of given amino acid types (for H2) or in given structural states (for T2), i...
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We examine how effectively simple potential functions previously developed can identify compatibilities between sequences and structures of proteins for database searches. The potential function consists of pairwise contact energies, repulsive packing potentials of residues for overly dense arrangement and short-range potentials for secondary structures, all of which were estimated from statist...
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Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming meth...
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ژورنال
عنوان ژورنال: Protein Science
سال: 2000
ISSN: 0961-8368,1469-896X
DOI: 10.1110/ps.9.8.1576