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Bioinformatics. 2014 Jun 1;30(11):1595-600. doi: 10.1093/bioinformatics/btu073. Epub 2014 Feb 3.

AMASS: a database for investigating protein structures.

Author information

1
Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USABiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USABiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
2
Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

Abstract

MOTIVATION:

Modern techniques have produced many sequence annotation databases and protein structure portals, but these Web resources are rarely integrated in ways that permit straightforward exploration of protein functional residues and their co-localization.

RESULTS:

We have created the AMASS database, which maps 1D sequence annotation databases to 3D protein structures with an intuitive visualization interface. Our platform also provides an analysis service that screens mass spectrometry sequence data for post-translational modifications that reside in functionally relevant locations within protein structures. The system is built on the premise that functional residues such as active sites, cancer mutations and post-translational modifications within proteins may co-localize and share common functions.

AVAILABILITY AND IMPLEMENTATION:

AMASS database is implemented with Biopython and Apache as a freely available Web server at amass-db.org.

PMID:
24497503
PMCID:
PMC4029036
DOI:
10.1093/bioinformatics/btu073
[Indexed for MEDLINE]
Free PMC Article
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