MSDmotif: exploring protein sites and motifs

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, ？/ψ 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.Small sequence or structure protein fragments with highly conserved properties that may have important biological functions and have been used in tertiary structure and secondary structure prediction processes [1,2]. Although the application of structure motifs to a sequence where the structure is unknown requires additional information such as a global energy function, structure motifs in combination with sequence motifs can be mapped onto structures [3,4]. In addition, sequence and structure motifs have an application in drug design [5] when motifs map to active-sites and ligand binding sites. We have created an integrated resource of information about motifs and their environme