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

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

Computer Science and Engineering

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

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 language	English (US)
Pages (from-to)	1595-1600
Number of pages	6
Journal	Bioinformatics
Volume	30
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btu073
State	Published - Jun 1 2014

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btu073

Cite this

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title = "AMASS: A database for investigating protein structures",

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:",

author = "Mielke, {Clinton J.} and Mandarino, {Lawrence J.} and Valentin Dinu",

note = "Funding Information: Funding: This work was supported by the National Institutes of Health [R01DK047936 to L.J.M.], Arizona State University, Mayo Clinic, and the Virginia G. Piper Charitable Trust (V.D.).",

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AU - Mandarino, Lawrence J.

AU - Dinu, Valentin

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AMASS: A database for investigating protein structures

Abstract

ASJC Scopus subject areas

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