A versatile structural domain analysis server using profile weight matrices

Steffen Schmidt; Peer Bork; Thomas Dandekar

doi:10.1021/ci010374r

A versatile structural domain analysis server using profile weight matrices

J Chem Inf Comput Sci. 2002 Mar-Apr;42(2):405-7. doi: 10.1021/ci010374r.

Authors

Steffen Schmidt¹, Peer Bork, Thomas Dandekar

Affiliation

¹ EMBL, Postfach 102209, D-69012 Heidelberg, Germany.

PMID: 11911710
DOI: 10.1021/ci010374r

Abstract

The WEB tool "AnDom" assigns to a given protein sequence all experimentally determined structural domains contained within it, including multidomain and large proteins. The server uses profile specific matrices from custom generated multiple sequence alignments of all known SCOP domains (SCOP version 1.50). Prediction time is short allowing numerous applications for structural genomics including investigation of complex eucaryotic protein families. The WWW server is at http://www.bork.embl-heidelberg.de/AnDom, and profiles can be downloaded at ftp.bork.embl-heidelberg.de/pub/users/ schmidt/AnDom.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Databases, Protein*
Molecular Sequence Data
Protein Conformation*
Proteins / chemistry*
Sequence Homology, Amino Acid

Substances

Proteins