Paper Info
Title
MSDmotif: exploring protein sites and motifs.
Abstract
Protein structures have conserved features - motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB) is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure.We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, phi/psi sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS) protocol. An additional entry point facilitates XML requests with XML responses.MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.
Year
DOI
Venue
2008
10.1186/1471-2105-9-312
BMC Bioinformatics
Keywords
Field
DocType
visual search,sequence motif,protein sequence,database management systems,amino acid,computer graphics,multiple alignment,microarrays,bioinformatics,algorithms,secondary structure,statistical distribution,ligand binding,protein data bank,predictive modelling,drug design,integrable system,binding sites,search engine,proteins,protein structure
Protein structure prediction,Binding site,Biology,Protein sequencing,Bioinformatics,Protein Data Bank,Protein Data Bank (RCSB PDB),Protein function prediction,DNA microarray,Protein structure
Journal
Volume
Issue
ISSN
9
1
1471-2105
Citations 
PageRank 
References 
55
2.35
23
Authors
2
Name
Order
Citations
PageRank
A Golovin125149.07
Kim Henrick255379.58