title: MetalPDB: a database of metal sites in biological macromolecular structures.
abstract: We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.
authors.affiliation: Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy. andreini@cerm.unifi.it
authors.forename: Claudia
authors.initials: C
authors.lastname: Andreini
authors.forename: Gabriele
authors.initials: G
authors.lastname: Cavallaro
authors.forename: Serena
authors.initials: S
authors.lastname: Lorenzini
authors.forename: Antonio
authors.initials: A
authors.lastname: Rosato
mesh_terms: D001665:Binding Sites; D062126:Databases, Chemical; D020407:Internet; D008667:Metalloproteins / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D009696:Nucleic Acids / Q000737:chemistry*; D014584:User-Computer Interface
chemical_list: D008667:Metalloproteins; D008670:Metals; D009696:Nucleic Acids