Title

DECOMP: A PDB decomposition tool on the web

Authors

Rafael Ordog^1,2, Zoltán Szabadka^1,2,3, Vince Grolmusz^{1,2 *}

Affiliation

¹Protein Information Technology Group, Eötvös University, 1117 Budapest, Hungary; ²Uratim Ltd. 4400 Nyíregyháza, Hungary; 3Google Inc, Europe

Email

grolmusz@cs.elte.hu

Article Type

Web Server

Date

Received February 22, 2009; accepted May 22, 2009; published July 27, 2009

Abstract

The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi-monomer ligands, and the server also offers the preprocessed ligand-protein decomposition of the complete PDB for downloading (up to size: 5GB).

Keywords

PDB, web tool, decomposition, server, ligands, SEQRES

Citation

Ordog et al, Bioinformation 3(10): 413-414 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.