MetalPDB: a database of metal sites in biological macromolecular structures

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 systemat...

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Bibliographic Details
Published in:Nucleic acids research 2013-01, Vol.41 (Database issue), p.D312-D319
Main Authors: Andreini, Claudia, Cavallaro, Gabriele, Lorenzini, Serena, Rosato, Antonio
Format: Article
Language:English
Subjects:
Binding Sites
Databases, Chemical
Internet
Metalloproteins - chemistry
Metals - chemistry
Models, Molecular
Nucleic Acids - chemistry
User-Computer Interface
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gks1063