RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances

Bittrich, Sebastian; Bhikadiya, Charmi; Bi, Chunxiao; Chao, Henry; Duarte, Jose M.; Dutta, Shuchismita; Fayazi, Maryam; Henry, Jeremy; Khokhriakov, Igor; Lowe, Robert; Piehl, Dennis W.; Segura, Joan; Vallat, Brinda; Voigt, Maria; Westbrook, John D.; Burley, Stephen K.; Rose, Yana

doi:10.1016/j.jmb.2023.167994

Title: RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances

Publication Date:: Sat Jul 01 00:00:00 EDT 2023

Sponsoring Org.:: USDOE

OSTI Identifier:: 1963124

Grant/Contract Number:: SC0019749

Resource Type:: Published Article

Journal Name:: Journal of Molecular Biology

Additional Journal Information:: Journal Name: Journal of Molecular Biology Journal Volume: 435 Journal Issue: 14; Journal ID: ISSN 0022-2836

Publisher:: Elsevier

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Bittrich, Sebastian, Bhikadiya, Charmi, Bi, Chunxiao, Chao, Henry, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Henry, Jeremy, Khokhriakov, Igor, Lowe, Robert, Piehl, Dennis W., Segura, Joan, Vallat, Brinda, Voigt, Maria, Westbrook, John D., Burley, Stephen K., and Rose, Yana. RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.  United Kingdom: N. p., 2023. 
Web.  doi:10.1016/j.jmb.2023.167994.

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                    Bittrich, Sebastian, Bhikadiya, Charmi, Bi, Chunxiao, Chao, Henry, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Henry, Jeremy, Khokhriakov, Igor, Lowe, Robert, Piehl, Dennis W., Segura, Joan, Vallat, Brinda, Voigt, Maria, Westbrook, John D., Burley, Stephen K., & Rose, Yana. RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.  United Kingdom.  https://doi.org/10.1016/j.jmb.2023.167994

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                    Bittrich, Sebastian, Bhikadiya, Charmi, Bi, Chunxiao, Chao, Henry, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Henry, Jeremy, Khokhriakov, Igor, Lowe, Robert, Piehl, Dennis W., Segura, Joan, Vallat, Brinda, Voigt, Maria, Westbrook, John D., Burley, Stephen K., and Rose, Yana. Sat .  
"RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances".  United Kingdom.  https://doi.org/10.1016/j.jmb.2023.167994.

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@article{osti_1963124,

  title        = {RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances},

  author       = {Bittrich, Sebastian and Bhikadiya, Charmi and Bi, Chunxiao and Chao, Henry and Duarte, Jose M. and Dutta, Shuchismita and Fayazi, Maryam and Henry, Jeremy and Khokhriakov, Igor and Lowe, Robert and Piehl, Dennis W. and Segura, Joan and Vallat, Brinda and Voigt, Maria and Westbrook, John D. and Burley, Stephen K. and Rose, Yana},

  abstractNote = {},

  doi          = {10.1016/j.jmb.2023.167994},

  journal      = {Journal of Molecular Biology},

  number       = 14,

  volume       = 435,

  place        = {United Kingdom},

  year         = {Sat Jul 01 00:00:00 EDT 2023},

  month        = {Sat Jul 01 00:00:00 EDT 2023}

}

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Works referenced in this record:

Dali server: structural unification of protein families
journal, May 2022

Holm, Liisa
Nucleic Acids Research, Vol. 50, Issue W1
DOI: 10.1093/nar/gkac387

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

Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar
Nucleic Acids Research, Vol. 49, Issue W1
DOI: 10.1093/nar/gkab314

Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
journal, March 1978

Garnier, J.; Osguthorpe, D. J.; Robson, B.
Journal of Molecular Biology, Vol. 120, Issue 1
DOI: 10.1016/0022-2836(78)90297-8

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies
journal, May 2022

Segura, Joan; Rose, Yana; Bittrich, Sebastian
Bioinformatics, Vol. 38, Issue 12
DOI: 10.1093/bioinformatics/btac317

BioJava 5: A community driven open-source bioinformatics library
journal, February 2019

Lafita, Aleix; Bliven, Spencer; Prlić, Andreas
PLOS Computational Biology, Vol. 15, Issue 2
DOI: 10.1371/journal.pcbi.1006791

Real-time structure search and structure classification for AlphaFold protein models
journal, April 2022

Aderinwale, Tunde; Bharadwaj, Vijay; Christoffer, Charles
Communications Biology, Vol. 5, Issue 1
DOI: 10.1038/s42003-022-03261-8

UniProt: the universal protein knowledgebase in 2021
journal, November 2020

Bateman, Alex; Martin, Maria-Jesus; Orchard, Sandra
Nucleic Acids Research, Vol. 49, Issue D1
DOI: 10.1093/nar/gkaa1100

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level
journal, October 2022

Shao, Chenghua; Bittrich, Sebastian; Wang, Sijian
Structure, Vol. 30, Issue 10
DOI: 10.1016/j.str.2022.08.004

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
journal, October 2017

Steinegger, Martin; Söding, Johannes
Nature Biotechnology, Vol. 35, Issue 11
DOI: 10.1038/nbt.3988

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
journal, November 2022

Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao
Nucleic Acids Research, Vol. 51, Issue D1
DOI: 10.1093/nar/gkac1077

Correlated mutations and residue contacts in proteins
journal, April 1994

Göbel, Ulrike; Sander, Chris; Schneider, Reinhard
Proteins: Structure, Function, and Genetics, Vol. 18, Issue 4
DOI: 10.1002/prot.340180402

Accurate prediction of protein structures and interactions using a three-track neural network
journal, July 2021

Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan
Science, Vol. 373, Issue 6557
DOI: 10.1126/science.abj8754

Crystallography: Protein Data Bank
journal, October 1971

Skipper, Magdalena
Nature New Biology, Vol. 233, Issue 42, p. 223-223
DOI: 10.1038/newbio233223b0

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology
journal, June 2022

Westbrook, John D.; Young, Jasmine Y.; Shao, Chenghua
Journal of Molecular Biology, Vol. 434, Issue 11
DOI: 10.1016/j.jmb.2022.167599

TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures
journal, November 2022

Dobson, Laszlo; Szekeres, Levente I.; Gerdán, Csongor
Nucleic Acids Research, Vol. 51, Issue D1
DOI: 10.1093/nar/gkac928

Outcome of a Workshop on Applications of Protein Models in Biomedical Research
journal, February 2009

Schwede, Torsten; Sali, Andrej; Honig, Barry
Structure, Vol. 17, Issue 2
DOI: 10.1016/j.str.2008.12.014

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
journal, March 2017

Young, Jasmine Y.; Westbrook, John D.; Feng, Zukang
Structure, Vol. 25, Issue 3
DOI: 10.1016/j.str.2017.01.004

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
journal, November 2021

Varadi, Mihaly; Anyango, Stephen; Deshpande, Mandar
Nucleic Acids Research, Vol. 50, Issue D1
DOI: 10.1093/nar/gkab1061

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management
journal, October 2020

Sehnal, David; Bittrich, Sebastian; Velankar, Sameer
PLOS Computational Biology, Vol. 16, Issue 10
DOI: 10.1371/journal.pcbi.1008247

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
journal, August 2013

Mariani, Valerio; Biasini, Marco; Barbato, Alessandro
Bioinformatics, Vol. 29, Issue 21
DOI: 10.1093/bioinformatics/btt473

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

Rose, Yana; Duarte, Jose M.; Lowe, Robert
Journal of Molecular Biology
DOI: 10.1016/j.jmb.2020.11.003

Highly accurate protein structure prediction with AlphaFold
journal, July 2021

Jumper, John; Evans, Richard; Pritzel, Alexander
Nature
DOI: 10.1038/s41586-021-03819-2

Real-time structural motif searching in proteins using an inverted index strategy
journal, December 2020

Bittrich, Sebastian; Burley, Stephen K.; Rose, Alexander S.
PLOS Computational Biology, Vol. 16, Issue 12
DOI: 10.1371/journal.pcbi.1008502

Combining evolutionary information and neural networks to predict protein secondary structure
journal, May 1994

Rost, Burkhard; Sander, Chris
Proteins: Structure, Function, and Genetics, Vol. 19, Issue 1
DOI: 10.1002/prot.340190108

The relation between the divergence of sequence and structure in proteins.
journal, April 1986

Chothia, C.; Lesk, A. M.
The EMBO Journal, Vol. 5, Issue 4
DOI: 10.1002/j.1460-2075.1986.tb04288.x

Critical assessment of methods of protein structure prediction (CASP)—Round XIV
journal, October 2021

Kryshtafovych, Andriy; Schwede, Torsten; Topf, Maya
Proteins: Structure, Function, and Bioinformatics
DOI: 10.1002/prot.26237

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
journal, January 2003

Boeckmann, B.
Nucleic Acids Research, Vol. 31, Issue 1
DOI: 10.1093/nar/gkg095

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

Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao
Nucleic Acids Research, Vol. 49, Issue D1
DOI: 10.1093/nar/gkaa1038

Real time structural search of the Protein Data Bank
journal, July 2020

Guzenko, Dmytro; Burley, Stephen K.; Duarte, Jose M.
PLOS Computational Biology, Vol. 16, Issue 7
DOI: 10.1371/journal.pcbi.1007970

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB
journal, December 2021

Bittrich, Sebastian; Rose, Yana; Segura, Joan
Bioinformatics, Vol. 38, Issue 5
DOI: 10.1093/bioinformatics/btab813

Protein Data Bank: the single global archive for 3D macromolecular structure data
journal, October 2018

Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
Nucleic Acids Research, Vol. 47, Issue D1
DOI: 10.1093/nar/gky949

Computed structures of core eukaryotic protein complexes
journal, December 2021

Humphreys, Ian R.; Pei, Jimin; Baek, Minkyung
Science, Vol. 374, Issue 6573
DOI: 10.1126/science.abm4805

Cryo-EM: The Resolution Revolution and Drug Discovery
journal, January 2021

de Oliveira, Taiana Maia; van Beek, Lotte; Shilliday, Fiona
SLAS Discovery, Vol. 26, Issue 1
DOI: 10.1177/2472555220960401

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

Segura, Joan; Rose, Yana; Westbrook, John
Bioinformatics, Vol. 36, Issue 22-23
DOI: 10.1093/bioinformatics/btaa1012

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
journal, November 2021

Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao
Protein Science, Vol. 31, Issue 1
DOI: 10.1002/pro.4213

Protein 3D Structure Computed from Evolutionary Sequence Variation
journal, December 2011

Marks, Debora S.; Colwell, Lucy J.; Sheridan, Robert
PLoS ONE, Vol. 6, Issue 12
DOI: 10.1371/journal.pone.0028766

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students
journal, October 2022

Burley, Stephen K.; Berman, Helen M.; Duarte, Jose M.
Biomolecules, Vol. 12, Issue 10
DOI: 10.3390/biom12101425

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Citation Formats

Dali server: structural unification of protein families journal, May 2022

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

Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins journal, March 1978

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Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
journal, March 1978

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journal, May 2022

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journal, November 2022

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journal, October 1971

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journal, June 2022

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journal, July 2021

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journal, December 2020

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