Topology independent protein structural alignment
نویسندگان
چکیده
منابع مشابه
Approximate protein structural alignment in polynomial time.
Alignment of protein structures is a fundamental task in computational molecular biology. Good structural alignments can help detect distant evolutionary relationships that are hard or impossible to discern from protein sequences alone. Here, we study the structural alignment problem as a family of optimization problems and develop an approximate polynomial-time algorithm to solve them. For a c...
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Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence...
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MOTIVATION This work aims to develop computational methods to annotate protein structures in an automated fashion. We employ a support vector machine (SVM) classifier to map from a given class of structures to their corresponding structural (SCOP) or functional (Gene Ontology) annotation. In particular, we build upon recent work describing various kernels for protein structures, where a kernel ...
متن کاملProtein Structure Alignment through a Contact Topology Profile using SABERTOOTH
The contact vector (CV) of a protein structure is one of the simplest and most condensed descriptions of protein structure available. It lists the number of contacts each amino acid has with the surrounding structure and has frequently been used e.g. to derive approximative folding energies in protein folding analysis. The CV, however, is a lossy structure representation, as it does not contain...
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BACKGROUND Although Transmembrane Proteins (TMPs) are highly important in various biological processes and pharmaceutical developments, general prediction of TMP structures is still far from satisfactory. Because TMPs have significantly different physicochemical properties from soluble proteins, current protein structure prediction tools for soluble proteins may not work well for TMPs. With the...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2007
ISSN: 1471-2105
DOI: 10.1186/1471-2105-8-388