Literature DB >> 34676613

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

Stephen K Burley1,2,3,4,5, Charmi Bhikadiya1,2, Chunxiao Bi4, Sebastian Bittrich4, Li Chen1,2, Gregg V Crichlow1,2, Jose M Duarte4, Shuchismita Dutta1,2,3, Maryam Fayazi1,2, Zukang Feng1,2, Justin W Flatt1,2, Sai J Ganesan6, David S Goodsell1,2,3,7, Sutapa Ghosh1,2, Rachel Kramer Green1,2, Vladimir Guranovic1,2, Jeremy Henry4, Brian P Hudson1,2, Catherine L Lawson1,2, Yuhe Liang1,2, Robert Lowe1,2, Ezra Peisach1,2, Irina Persikova1,2, Dennis W Piehl1,2, Yana Rose4, Andrej Sali6, Joan Segura4, Monica Sekharan1,2, Chenghua Shao1,2, Brinda Vallat1,2, Maria Voigt1,2, John D Westbrook1,2,3, Shamara Whetstone1,2, Jasmine Y Young1,2, Christine Zardecki1,2.   

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.
© 2021 The Protein Society.

Entities:  

Keywords:  Mol*; PDB; Protein Data Bank; RCSB Protein Data Bank; Worldwide Protein Data Bank; electron microscopy; macromolecular crystallography; micro-electron diffraction; open access; web-native molecular graphics

Mesh:

Year:  2021        PMID: 34676613      PMCID: PMC8740825          DOI: 10.1002/pro.4213

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  85 in total

1.  Escape from lysosomes.

Authors: 
Journal:  Nat New Biol       Date:  1971-10-20

2.  Retrieval of crystallographically-derived molecular geometry information.

Authors:  Ian J Bruno; Jason C Cole; Magnus Kessler; Jie Luo; W D Sam Motherwell; Lucy H Purkis; Barry R Smith; Robin Taylor; Richard I Cooper; Stephanie E Harris; A Guy Orpen
Journal:  J Chem Inf Comput Sci       Date:  2004 Nov-Dec

3.  OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Authors:  Jasmine Y Young; John D Westbrook; Zukang Feng; Raul Sala; Ezra Peisach; Thomas J Oldfield; Sanchayita Sen; Aleksandras Gutmanas; David R Armstrong; John M Berrisford; Li Chen; Minyu Chen; Luigi Di Costanzo; Dimitris Dimitropoulos; Guanghua Gao; Sutapa Ghosh; Swanand Gore; Vladimir Guranovic; Pieter M S Hendrickx; Brian P Hudson; Reiko Igarashi; Yasuyo Ikegawa; Naohiro Kobayashi; Catherine L Lawson; Yuhe Liang; Steve Mading; Lora Mak; M Saqib Mir; Abhik Mukhopadhyay; Ardan Patwardhan; Irina Persikova; Luana Rinaldi; Eduardo Sanz-Garcia; Monica R Sekharan; Chenghua Shao; G Jawahar Swaminathan; Lihua Tan; Eldon L Ulrich; Glen van Ginkel; Reiko Yamashita; Huanwang Yang; Marina A Zhuravleva; Martha Quesada; Gerard J Kleywegt; Helen M Berman; John L Markley; Haruki Nakamura; Sameer Velankar; Stephen K Burley
Journal:  Structure       Date:  2017-02-09       Impact factor: 5.006

4.  Landscape of Innovation for Cardiovascular Pharmaceuticals: From Basic Science to New Molecular Entities.

Authors:  Jennifer M Beierlein; Laura M McNamee; Michael J Walsh; Kenneth I Kaitin; Joseph A DiMasi; Fred D Ledley
Journal:  Clin Ther       Date:  2017-06-23       Impact factor: 3.393

5.  RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Jose M Duarte; Shuchismita Dutta; Maryam Fayazi; Zukang Feng; Justin W Flatt; Sai J Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranovic; Jeremy Henry; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Ezra Peisach; Irina Persikova; Dennis W Piehl; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Brinda Vallat; Maria Voigt; John D Westbrook; Shamara Whetstone; Jasmine Y Young; Christine Zardecki
Journal:  Protein Sci       Date:  2021-11-06       Impact factor: 6.725

6.  Manual classification strategies in the ECOD database.

Authors:  Hua Cheng; Yuxing Liao; R Dustin Schaeffer; Nick V Grishin
Journal:  Proteins       Date:  2015-05-08

7.  Fast determination of the optimal rotational matrix for macromolecular superpositions.

Authors:  Pu Liu; Dimitris K Agrafiotis; Douglas L Theobald
Journal:  J Comput Chem       Date:  2010-05       Impact factor: 3.376

8.  TM-align: a protein structure alignment algorithm based on the TM-score.

Authors:  Yang Zhang; Jeffrey Skolnick
Journal:  Nucleic Acids Res       Date:  2005-04-22       Impact factor: 16.971

9.  BioJava 5: A community driven open-source bioinformatics library.

Authors:  Aleix Lafita; Spencer Bliven; Andreas Prlić; Dmytro Guzenko; Peter W Rose; Anthony Bradley; Paolo Pavan; Douglas Myers-Turnbull; Yana Valasatava; Michael Heuer; Matt Larson; Stephen K Burley; Jose M Duarte
Journal:  PLoS Comput Biol       Date:  2019-02-08       Impact factor: 4.475

10.  Investigation of protein quaternary structure via stoichiometry and symmetry information.

Authors:  Selcuk Korkmaz; Jose M Duarte; Andreas Prlić; Dincer Goksuluk; Gokmen Zararsiz; Osman Saracbasi; Stephen K Burley; Peter W Rose
Journal:  PLoS One       Date:  2018-06-04       Impact factor: 3.240

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  13 in total

1.  RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Jose M Duarte; Shuchismita Dutta; Maryam Fayazi; Zukang Feng; Justin W Flatt; Sai J Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranovic; Jeremy Henry; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Ezra Peisach; Irina Persikova; Dennis W Piehl; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Brinda Vallat; Maria Voigt; John D Westbrook; Shamara Whetstone; Jasmine Y Young; Christine Zardecki
Journal:  Protein Sci       Date:  2021-11-06       Impact factor: 6.725

2.  The Extract of Ilex cornuta Bark Promotes Bone Healing by Activating Adenosine A2A Receptor.

Authors:  Xi Zheng; Jingyi Wang; Junlin Zhou; Dong Wang
Journal:  Drug Des Devel Ther       Date:  2022-08-04       Impact factor: 4.319

3.  Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.

Authors:  Chenghua Shao; Sebastian Bittrich; Sijian Wang; Stephen K Burley
Journal:  Structure       Date:  2022-08-31       Impact factor: 5.871

4.  Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions.

Authors:  Jeffrey Skolnick; Hongyi Zhou
Journal:  J Phys Chem B       Date:  2022-08-31       Impact factor: 3.466

5.  Catechin Mediates Ferroptosis to Exert an Anti-Inflammatory Effect on RAW 264.7 Cells.

Authors:  Weiyang Kuang; Jiajia Yang; Zhiyuan Liu; Jinzi Zeng; Xuewei Xia; Xiaodan Chen; Saiyi Zhong; Riming Huang
Journal:  Foods       Date:  2022-05-27

6.  Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements.

Authors:  Dolores Linde; Elena Santillana; Elena Fernández-Fueyo; Alejandro González-Benjumea; Juan Carro; Ana Gutiérrez; Angel T Martínez; Antonio Romero
Journal:  Antioxidants (Basel)       Date:  2022-04-30

7.  PDB-101: Educational resources supporting molecular explorations through biology and medicine.

Authors:  Christine Zardecki; Shuchismita Dutta; David S Goodsell; Robert Lowe; Maria Voigt; Stephen K Burley
Journal:  Protein Sci       Date:  2021-10-18       Impact factor: 6.725

8.  A roadmap for the functional annotation of protein families: a community perspective.

Authors:  Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J Bridge; Stephen K Burley; Stacey Cleveland; Lucy J Colwell; Ana Conesa; Christian Dallago; Antoine Danchin; Anita de Waard; Adam Deutschbauer; Raquel Dias; Yousong Ding; Gang Fang; Iddo Friedberg; John Gerlt; Joshua Goldford; Mark Gorelik; Benjamin M Gyori; Christopher Henry; Geoffrey Hutinet; Marshall Jaroch; Peter D Karp; Liudmyla Kondratova; Zhiyong Lu; Aron Marchler-Bauer; Maria-Jesus Martin; Claire McWhite; Gaurav D Moghe; Paul Monaghan; Anne Morgat; Christopher J Mungall; Darren A Natale; William C Nelson; Seán O'Donoghue; Christine Orengo; Katherine H O'Toole; Predrag Radivojac; Colbie Reed; Richard J Roberts; Dmitri Rodionov; Irina A Rodionova; Jeffrey D Rudolf; Lana Saleh; Gloria Sheynkman; Francoise Thibaud-Nissen; Paul D Thomas; Peter Uetz; David Vallenet; Erica Watson Carter; Peter R Weigele; Valerie Wood; Elisha M Wood-Charlson; Jin Xu
Journal:  Database (Oxford)       Date:  2022-08-12       Impact factor: 4.462

9.  Exploring protein symmetry at the RCSB Protein Data Bank.

Authors:  Jose M Duarte; Shuchismita Dutta; David S Goodsell; Stephen K Burley
Journal:  Emerg Top Life Sci       Date:  2022-09-09

10.  Synthesis and Structural Characterization of Pyridine-2,6-dicarboxamide and Furan-2,5-dicarboxamide Derivatives.

Authors:  Anna Puckowska; Magdalena Gawel; Marlena Komorowska; Pawel Drozdzal; Aleksandra Arning; Damian Pawelski; Krzysztof Brzezinski; Marta E Plonska-Brzezinska
Journal:  Molecules       Date:  2022-03-10       Impact factor: 4.411

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