Identifying structural domains of proteins using clustering
نویسندگان
چکیده
منابع مشابه
Identifying structural domains in proteins.
Analysis of protein structures typically beginswith decomposition of the structure intomore basic units called structural domains. The underlying goal is to reduce a complex protein structure to a set of simpler, yet structurallymeaningful units, each ofwhich can be analyzed independently. Structural semi-independence of domains is their hallmark: domains often have compact structure that can f...
متن کاملIdentifying Structural Motifs in Proteins
In biological macromolecules, structural patterns (motifs) are often repeated across different molecules. Detection of these common motifs in a new molecule can provide useful clues to the functional properties of such a molecule. We formulate the problem of identifying a given structural motif (pattern) in a target protein (example) and discuss the notion of complete matches vis-a-vis partial ...
متن کاملDOMIRE: a web server for identifying structural domains and their neighbors in proteins
SUMMARY The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are...
متن کاملCHOP: parsing proteins into structural domains
Sequence-based domain assignment is one of the most important and challenging problems in structural biology. We have developed a method, CHOP, that chops proteins into domain-like fragments. The basic idea is to cut proteins from entirely sequenced organisms beginning from very reliable experimental information (Protein Data Bank), proceeding to expert annotations of domain-like regions (Pfam-...
متن کاملToward consistent assignment of structural domains in proteins.
The assignment of protein domains from three-dimensional structure is critically important in understanding protein evolution and function, yet little quality assurance has been performed. Here, the differences in the assignment of structural domains are evaluated using six common assignment methods. Three human expert methods (AUTHORS (authors' annotation), CATH and SCOP) and three fully autom...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2012
ISSN: 1471-2105
DOI: 10.1186/1471-2105-13-286