RCSB Protein Data Bank 1D tools and services

Joan Segura; Yana Rose; John Westbrook; Stephen K Burley; Jose M Duarte

doi:10.1093/bioinformatics/btaa1012

RCSB Protein Data Bank 1D tools and services

Bioinformatics. 2021 Apr 1;36(22-23):5526-5527. doi: 10.1093/bioinformatics/btaa1012.

Authors

Joan Segura¹, Yana Rose¹, John Westbrook^{1

2

3}, Stephen K Burley^{1

2

3

4

5}, Jose M Duarte¹

Affiliations

¹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
² Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
³ Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁴ Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁵ Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.

Abstract

Motivation: Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function.

Results: Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web.

Availabilityand implementation: https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro.

Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract

Grants and funding