AMASS: a database for investigating protein structures

Clinton J Mielke; Lawrence J Mandarino; Valentin Dinu

doi:10.1093/bioinformatics/btu073

AMASS: a database for investigating protein structures

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

Authors

Clinton J Mielke¹, Lawrence J Mandarino², Valentin Dinu²

Affiliations

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Databases, Protein*
Humans
Internet
Mass Spectrometry
Mitochondrial Proton-Translocating ATPases / chemistry
Molecular Sequence Annotation
Protein Conformation*
Protein Processing, Post-Translational
Proteins / chemistry
Proteins / genetics
Pyruvate Dehydrogenase Complex / chemistry
Sequence Analysis, Protein

Substances

ATP5F1B protein, human
Proteins
Pyruvate Dehydrogenase Complex
Mitochondrial Proton-Translocating ATPases

Abstract

Publication types

MeSH terms

Substances

Grants and funding