title: A tool to assist the study of specific features at protein binding sites.
abstract: 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
authors.affiliation: Pontificia Universidad Católica de Chile, Departmento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Alameda 340, Santiago, Chile.
authors.forename: Víctor
authors.initials: V
authors.lastname: Santander
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Portales
authors.forename: Francisco
authors.initials: F
authors.lastname: Melo
mesh_terms: D001665:Binding Sites; D003628:Database Management Systems; D030562:Databases, Protein; D033181:Information Dissemination / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
chemical_list: D011506:Proteins