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

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

Abstract

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.

Authors:

; Rose, Yana; Segura, Joan; Lowe, Robert;

;

; Burley, Stephen K.; Valencia, ed., Alfonso

Publication Date:: Thu Dec 02 00:00:00 EST 2021

Research Org.:: Univ. of California, La Jolla, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1844289

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

Grant/Contract Number:: SC0019749; R01GM133198

Resource Type:: Published Article

Journal Name:: Bioinformatics

Additional Journal Information:: Journal Name: Bioinformatics Journal Volume: 38 Journal Issue: 5; Journal ID: ISSN 1367-4803

Publisher:: Oxford University Press

Country of Publication:: United Kingdom

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Bittrich, Sebastian, Rose, Yana, Segura, Joan, Lowe, Robert, Westbrook, John D., Duarte, Jose M., Burley, Stephen K., and Valencia, ed., Alfonso. RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.  United Kingdom: N. p., 2021. 
Web.  doi:10.1093/bioinformatics/btab813.

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                    Bittrich, Sebastian, Rose, Yana, Segura, Joan, Lowe, Robert, Westbrook, John D., Duarte, Jose M., Burley, Stephen K., & Valencia, ed., Alfonso. RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.  United Kingdom.  https://doi.org/10.1093/bioinformatics/btab813

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                    Bittrich, Sebastian, Rose, Yana, Segura, Joan, Lowe, Robert, Westbrook, John D., Duarte, Jose M., Burley, Stephen K., and Valencia, ed., Alfonso. Thu .  
"RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB".  United Kingdom.  https://doi.org/10.1093/bioinformatics/btab813.

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@article{osti_1844289,

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

  author       = {Bittrich, Sebastian and Rose, Yana and Segura, Joan and Lowe, Robert and Westbrook, John D. and Duarte, Jose M. and Burley, Stephen K. and Valencia, ed., Alfonso},

  abstractNote = {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.},

  doi          = {10.1093/bioinformatics/btab813},

  journal      = {Bioinformatics},

  number       = 5,

  volume       = 38,

  place        = {United Kingdom},

  year         = {Thu Dec 02 00:00:00 EST 2021},

  month        = {Thu Dec 02 00:00:00 EST 2021}

}

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Works referenced in this record:

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Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar
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Nucleic Acids Research, Vol. 41, Issue D1
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Shimizu, Kentaro; Cao, Wei; Saad, Gull
Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1860, Issue 5
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Title: RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Abstract

Citation Formats

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures journal, May 2021

Transmembrane proteins in the Protein Data Bank: identification and classification journal, June 2004

Membrane positioning for high- and low-resolution protein structures through a binary classification approach journal, December 2015

Biophysical dissection of membrane proteins journal, May 2009

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions journal, November 2018

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive journal, November 2020

RCSB Protein Data Bank 1D tools and services journal, December 2020

OPM database and PPM web server: resources for positioning of proteins in membranes journal, September 2011

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences journal, November 2020

PDBTM: Protein Data Bank of transmembrane proteins after 8 years journal, November 2012

Comparative analysis of membrane protein structure databases journal, May 2018

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
journal, May 2021

Transmembrane proteins in the Protein Data Bank: identification and classification
journal, June 2004

Membrane positioning for high- and low-resolution protein structures through a binary classification approach
journal, December 2015

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journal, November 2018

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive
journal, November 2020

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OPM database and PPM web server: resources for positioning of proteins in membranes
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journal, November 2020

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