Structure-dependent sequence alignment for remotely related proteins
نویسندگان
چکیده
منابع مشابه
NdPASA: a pairwise sequence alignment server for distantly related proteins
SUMMARY NdPASA is a web server specifically designed to optimize sequence alignment between distantly related proteins. The program integrates structure information of the template sequence into a global alignment algorithm by employing neighbor-dependent propensities of amino acids as a unique parameter for alignment. NdPASA optimizes alignment by evaluating the likelihood of a residue pair in...
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A protein sequence-structure alignment method for database searches is examined on how effectively this method together with a simple scoring function previously developed can identify compatibilities between sequences and structures of proteins. The scoring function consists of pairwise contact energies, repulsive packing potentials of residues for overly dense arrangement and short-range pote...
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UNLABELLED Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence-structure-function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA soft...
متن کاملMMM: a sequence-to-structure alignment protocol
MOTIVATION Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models. RESULTS Multiple Mapping Method (MMM) is a comparative protein structure modeling server with an emphasis on a novel alignment optimization protocol. MMM takes inputs from five profile-to-profile based alignment methods. The al...
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The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix.
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2002
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/18.12.1658