Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

Andreas Prlic; Tara Kalro; Roshni Bhattacharya; Cole Christie; Stephen K Burley; Peter W Rose

doi:10.1093/bioinformatics/btw547

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Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

Journal article

Open access

Peer reviewed

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

Andreas Prlic, Tara Kalro, Roshni Bhattacharya, Cole Christie, Stephen K Burley and Peter W Rose

Bioinformatics (Oxford, England), Vol.32(24), pp.3833-3835

12/15/2016

DOI: https://doi.org/10.1093/bioinformatics/btw547

PMCID: PMC5167066

PMID: 27551105

Abstract

Amino Acid Sequence

Computational Biology - methods

Computer Graphics

Databases, Protein

Genomics

Humans

Protein Conformation

Software

User-Computer Interface

The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics. The new views are available from http://www.rcsb.org and software is available from https://github.com/rcsb/. andreas.prlic@rcsb.orgSupplementary information: Supplementary data are available at Bioinformatics online.

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Title: Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank
Creators: Andreas Prlic - RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA
Tara Kalro - RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA
Roshni Bhattacharya - Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA 92182, USA
Cole Christie - RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA
Stephen K Burley - RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, and Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Peter W Rose - RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA
Publication Details: Bioinformatics (Oxford, England), Vol.32(24), pp.3833-3835
Date published: 12/15/2016
Academic Unit: Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine
Language: English
Resource Type: Journal article
Identifiers: 991031665865304646