PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
نویسندگان
چکیده
منابع مشابه
PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL
MOTIVATION The recently released PyMod GUI integrates many of the individual steps required for protein sequence-structure analysis and homology modeling within the interactive visualization capabilities of PyMOL. Here we describe the improvements introduced into the version 2.0 of PyMod. RESULTS The original code of PyMod has been completely rewritten and improved in version 2.0 to extend Py...
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Every sequence comparison method requires a set of scores. For aligning protein sequences, substitution scores are based on models of amino acid conservation and properties, and matrices of these scores have substantially improved in recent years. Position-specific scoring matrices provide representations of sequence families that are capable of detecting subtle similarities. Comprehensive eval...
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Most bioinformatics analyses require the assembly of a multiple sequence alignment. It has long been suspected that structural information can help to improve the quality of these alignments, yet the effect of combining sequences and structures has not been evaluated systematically. We developed 3DCoffee, a novel method for combining protein sequences and structures in order to generate high-qu...
متن کاملFaster sequence homology searches by clustering subsequences
MOTIVATION Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. RESULTS We developed a fast homology search method based on database subsequence clusteri...
متن کاملComparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
MOTIVATION Two major bottlenecks in advancing comparative protein structure modeling are the efficient combination of multiple template structures and the generation of a correct input target-template alignment. RESULTS A novel method, Multiple Mapping Method with Multiple Templates (M4T) is introduced that implements an algorithm to automatically select and combine Multiple Template structur...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2012
ISSN: 1471-2105
DOI: 10.1186/1471-2105-13-s4-s2