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Advances in Bioinformatics
Volume 2010, Article ID 436036, 9 pages
http://dx.doi.org/10.1155/2010/436036
Research Article

PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools

1Biomedical Informatics Center, PGIMER, Chandigarh 160012, India
2Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
3Department of Nephrology, PGIMER, Chandigarh 160012, India
4National Institute of Biomedical Innovation, Department of Biomedical Research, Saito-Asagi, Ibaraki, Osaka 5670085, Japan

Received 11 February 2010; Revised 17 April 2010; Accepted 27 April 2010

Academic Editor: Janusz M. Bujnicki

Copyright © 2010 Adeel Malik et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins) as well as noncovalently (protein-carbohydrate complexes) is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i) Core PROCARB module, consisting of three-dimensional structures of protein-carbohydrate complexes taken from Protein Data Bank (PDB), (ii) Homology Models module, consisting of manually developed three-dimensional models of N-linked and O-linked glycoproteins of unknown three-dimensional structure, and (iii) CBS-Pred prediction module, consisting of web servers to predict carbohydrate-binding sites using single sequence or server-generated PSSM. Several precomputed structural and functional properties of complexes are also included in the database for quick analysis. In particular, information about function, secondary structure, solvent accessibility, hydrogen bonds and literature reference, and so forth, is included. In addition, each protein in the database is mapped to Uniprot, Pfam, PDB, and so forth.