Identifying sequence–structure pairs undetected by sequence alignments
نویسندگان
چکیده
منابع مشابه
Identifying sequence-structure pairs undetected by sequence alignments.
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...
متن کاملUse 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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SUMMARY SEGID is a tool for finding conserved regions (regions of high scores) for a given (multiple) sequence alignment. It takes a (multiple) sequence alignment as its input and converts the alignment into a sequence of numbers, where each number is the alignment score of a column. Three algorithms are used to identify regions of high scores. A graphical interface is provided to present those...
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We evaluate the performance of common substitution matrices with respect to structural similarities. For this purpose, we apply an all-versus-all pairwise sequence alignment on the ASTRAL40 [7] dataset, consisting of 7290 entries with a pairwise sequence identity of at most 40%. Afterwards, we compare the 100 highest scoring sequence alignments to their corresponding structural alignments, whic...
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MOTIVATION As sequence databases grow rapidly, results from sequence comparison searches using fast search methods such as BLAST and FASTA tend to be long and difficult to digest. RESULTS In this paper, we present a new method to extract domain information from sequence comparison searches by clustering the resulting alignments according to their similarity to the query sequence. Efficient tr...
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ژورنال
عنوان ژورنال: Protein Engineering, Design and Selection
سال: 2000
ISSN: 1741-0134,1741-0126
DOI: 10.1093/protein/13.7.459