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Bioinformatics Vol. 19 Suppl. 1 2003
Pages i250-i251
© 2003 Oxford University Press

A tool to assist the study of specific features at protein binding sites

Víctor Santander , Miguel Angel Portales and Francisco Melo *

Pontificia Universidad Católica de Chile, Departmento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Alameda 340, Santiago, Chile

Received on January 6, 2003 ; accepted on February 20, 2003

The Protein Data Bank contains a large amount of proteins that have been solved with small ligands bound to them. This constitutes a rich source of information for the study of the specific requirements of protein sites to bind small molecules with a favorable free energy. The specific atomic composition and three-dimensional geometric restraints of protein binding sites for different ligands could be easily obtained from there. The development of accurate binding site descriptors in proteins constitutes a valuable tool to assist in the large-scale prediction and annotation of protein function in whole genomes. In this work, an integrated database containing some processed and calculated protein/ligand information is described. It is expected that this database will constitute a useful tool for people working in the prediction of protein function from its structure. The database is accessible from the Internet through a web server located at: http://protein.bio.puc.cl

Contact: fmelo{at}genes.bio.puc.cl

Keywords: Ligands, function, structure, proteins, binding sites, conformational analysis

* To whom correspondence should be addressed.


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