MetalPDB in 2018: a database of metal sites in biological macromolecular structures.
Nucleic Acids Res
; 46(D1): D459-D464, 2018 01 04.
Article
em En
| MEDLINE
| ID: mdl-29077942
ABSTRACT
MetalPDB (http//metalweb.cerm.unifi.it/) is a database providing information on metal-binding sites detected in the three-dimensional (3D) structures of biological macromolecules. MetalPDB represents such sites as 3D templates, called Minimal Functional Sites (MFSs), which describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. The 2018 update of MetalPDB includes new contents and tools. A major extension is the inclusion of proteins whose structures do not contain metal ions although their sequences potentially contain a known MFS. In addition, MetalPDB now provides extensive statistical analyses addressing several aspects of general metal usage within the PDB, across protein families and in catalysis. Users can also query MetalPDB to extract statistical information on structural aspects associated with individual metals, such as preferred coordination geometries or aminoacidic environment. A further major improvement is the functional annotation of MFSs; the annotation is manually performed via a password-protected annotator interface. At present, â¼50% of all MFSs have such a functional annotation. Other noteworthy improvements are bulk query functionality, through the upload of a list of PDB identifiers, and ftp access to MetalPDB contents, allowing users to carry out in-depth analyses on their own computational infrastructure.
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1
Base de dados:
MEDLINE
Assunto principal:
Interface Usuário-Computador
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Metais Pesados
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Metais Leves
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Bases de Dados de Proteínas
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Substâncias Macromoleculares
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Metaloproteínas
Idioma:
En
Ano de publicação:
2018
Tipo de documento:
Article