AMASS: a database for investigating protein structures.
BACKGROUND
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.


METHODS
AMASS database is implemented with Biopython and Apache as a freely available Web server at amass-db.org.
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.
Clinton J
CJ
Mielke
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.
Lawrence J
LJ
Mandarino
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.
Valentin
V
Dinu
D030562:Databases, Protein; D006801:Humans; D020407:Internet; D013058:Mass Spectrometry; D025261:Mitochondrial Proton-Translocating ATPases / Q000737:chemistry; D058977:Molecular Sequence Annotation; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D011768:Pyruvate Dehydrogenase Complex / Q000737:chemistry; D020539:Sequence Analysis, Protein
C506526:ATP5F1B protein, human; D011506:Proteins; D011768:Pyruvate Dehydrogenase Complex; D025261:Mitochondrial Proton-Translocating ATPases