MSDmotif: exploring protein sites and motifs.

ABSTRACT:

Background

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.

Results

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 incor

SUBMITTER: Golovin A 

PROVIDER: S-EPMC2491636 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature