AMASS: A database for investigating protein structures

Clinton J. Mielke, Lawrence J. Mandarino, Valentin Dinu

Research output: Contribution to journalArticle

3 Citations (Scopus)

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. Contact:

Original languageEnglish (US)
Pages (from-to)1595-1600
Number of pages6
JournalBioinformatics
Volume30
Issue number11
DOIs
StatePublished - Jun 1 2014

Fingerprint

Protein Databases
Protein Structure
Databases
Post Translational Protein Processing
Proteins
Annotation
Protein
Mass Spectrometry
Catalytic Domain
Web Server
Intuitive
Cancer
Mutation
Visualization
Availability
World Wide Web
Mass spectrometry
Contact
Servers
Resources

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

AMASS : A database for investigating protein structures. / Mielke, Clinton J.; Mandarino, Lawrence J.; Dinu, Valentin.

In: Bioinformatics, Vol. 30, No. 11, 01.06.2014, p. 1595-1600.

Research output: Contribution to journalArticle

Mielke, Clinton J. ; Mandarino, Lawrence J. ; Dinu, Valentin. / AMASS : A database for investigating protein structures. In: Bioinformatics. 2014 ; Vol. 30, No. 11. pp. 1595-1600.
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