RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Bittrich, Sebastian; Rose, Yana; Segura, Joan; Lowe, Robert; Westbrook, John D.; Duarte, Jose M.; Burley, Stephen K.; Valencia, ed., Alfonso

doi:10.1093/bioinformatics/btab813

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Journal Article · Thu Dec 02 04:00:00 EST 2021 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btab813· OSTI ID:1844289

; Rose, Yana; Segura, Joan; Lowe, Robert; ; ; Burley, Stephen K.; Valencia, ed., Alfonso

Abstract Motivation

Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task.

Results

We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D.

Availability and implementation

Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar).

Supplementary information

Supplementary data are available at Bioinformatics online.

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0019749

OSTI ID:: 1844289

Alternate ID(s):: OSTI ID: 1835496
OSTI ID: 1846037

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 5 Vol. 38; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (11)

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