Literature DB >> 33211854

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.

Stephen K Burley1,2,3,4,5, Charmi Bhikadiya1,2, Chunxiao Bi4, Sebastian Bittrich4, Li Chen1,2, Gregg V Crichlow1,2, Cole H Christie4, Kenneth Dalenberg1,2, Luigi Di Costanzo1,2, Jose M Duarte4, Shuchismita Dutta1,2,3, Zukang Feng1,2, Sai Ganesan6, David S Goodsell1,2,7, Sutapa Ghosh1,2, Rachel Kramer Green1,2, Vladimir Guranović1,2, Dmytro Guzenko4, Brian P Hudson1,2, Catherine L Lawson1,2, Yuhe Liang1,2, Robert Lowe1,2, Harry Namkoong1,2, Ezra Peisach1,2, Irina Persikova1,2, Chris Randle4, Alexander Rose4, Yana Rose4, Andrej Sali6, Joan Segura4, Monica Sekharan1,2, Chenghua Shao1,2, Yi-Ping Tao1,2, Maria Voigt1,2, John D Westbrook1,2,3, Jasmine Y Young1,2, Christine Zardecki1,2, Marina Zhuravleva1,2.   

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Mesh:

Substances:

Year:  2021        PMID: 33211854      PMCID: PMC7779003          DOI: 10.1093/nar/gkaa1038

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  63 in total

1.  The PDB data uniformity project.

Authors:  T N Bhat; P Bourne; Z Feng; G Gilliland; S Jain; V Ravichandran; B Schneider; K Schneider; N Thanki; H Weissig; J Westbrook; H M Berman
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  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

3.  The RCSB Protein Data Bank: redesigned web site and web services.

Authors:  Peter W Rose; Bojan Beran; Chunxiao Bi; Wolfgang F Bluhm; Dimitris Dimitropoulos; David S Goodsell; Andreas Prlic; Martha Quesada; Gregory B Quinn; John D Westbrook; Jasmine Young; Benjamin Yukich; Christine Zardecki; Helen M Berman; Philip E Bourne
Journal:  Nucleic Acids Res       Date:  2010-10-29       Impact factor: 16.971

4.  PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Authors:  Saqib Mir; Younes Alhroub; Stephen Anyango; David R Armstrong; John M Berrisford; Alice R Clark; Matthew J Conroy; Jose M Dana; Mandar Deshpande; Deepti Gupta; Aleksandras Gutmanas; Pauline Haslam; Lora Mak; Abhik Mukhopadhyay; Nurul Nadzirin; Typhaine Paysan-Lafosse; David Sehnal; Sanchayita Sen; Oliver S Smart; Mihaly Varadi; Gerard J Kleywegt; Sameer Velankar
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

5.  DrugBank 5.0: a major update to the DrugBank database for 2018.

Authors:  David S Wishart; Yannick D Feunang; An C Guo; Elvis J Lo; Ana Marcu; Jason R Grant; Tanvir Sajed; Daniel Johnson; Carin Li; Zinat Sayeeda; Nazanin Assempour; Ithayavani Iynkkaran; Yifeng Liu; Adam Maciejewski; Nicola Gale; Alex Wilson; Lucy Chin; Ryan Cummings; Diana Le; Allison Pon; Craig Knox; Michael Wilson
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

6.  CATH: an expanded resource to predict protein function through structure and sequence.

Authors:  Natalie L Dawson; Tony E Lewis; Sayoni Das; Jonathan G Lees; David Lee; Paul Ashford; Christine A Orengo; Ian Sillitoe
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

7.  Analysis of impact metrics for the Protein Data Bank.

Authors:  Christopher Markosian; Luigi Di Costanzo; Monica Sekharan; Chenghua Shao; Stephen K Burley; Christine Zardecki
Journal:  Sci Data       Date:  2018-10-16       Impact factor: 6.444

8.  The RCSB Protein Data Bank: new resources for research and education.

Authors:  Peter W Rose; Chunxiao Bi; Wolfgang F Bluhm; Cole H Christie; Dimitris Dimitropoulos; Shuchismita Dutta; Rachel K Green; David S Goodsell; Andreas Prlic; Martha Quesada; Gregory B Quinn; Alexander G Ramos; John D Westbrook; Jasmine Young; Christine Zardecki; Helen M Berman; Philip E Bourne
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

9.  Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.

Authors:  Youngchang Kim; Robert Jedrzejczak; Natalia I Maltseva; Mateusz Wilamowski; Michael Endres; Adam Godzik; Karolina Michalska; Andrzej Joachimiak
Journal:  Protein Sci       Date:  2020-05-02       Impact factor: 6.993

10.  3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.

Authors:  Athri D Rathnayake; Jian Zheng; Yunjeong Kim; Krishani Dinali Perera; Samantha Mackin; David K Meyerholz; Maithri M Kashipathy; Kevin P Battaile; Scott Lovell; Stanley Perlman; William C Groutas; Kyeong-Ok Chang
Journal:  Sci Transl Med       Date:  2020-08-03       Impact factor: 17.956

View more
  186 in total

1.  Molecular storytelling for online structural biology outreach and education.

Authors:  David S Goodsell; Shuchismita Dutta; Maria Voigt; Christine Zardecki
Journal:  Struct Dyn       Date:  2021-03-05       Impact factor: 2.920

2.  Three-dimensional Structure Databases of Biological Macromolecules.

Authors:  Vaishali P Waman; Christine Orengo; Gerard J Kleywegt; Arthur M Lesk
Journal:  Methods Mol Biol       Date:  2022

3.  Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Authors:  Chenghua Shao; Zukang Feng; John D Westbrook; Ezra Peisach; John Berrisford; Yasuyo Ikegawa; Genji Kurisu; Sameer Velankar; Stephen K Burley; Jasmine Y Young
Journal:  Glycobiology       Date:  2021-09-20       Impact factor: 4.313

Review 4.  Experimental approaches for investigating ion atmospheres around nucleic acids and proteins.

Authors:  Binhan Yu; Junji Iwahara
Journal:  Comput Struct Biotechnol J       Date:  2021-04-17       Impact factor: 7.271

5.  PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors.

Authors:  Enade P Istyastono; Nunung Yuniarti; Vivitri D Prasasty; Sudi Mungkasi
Journal:  Molecules       Date:  2021-04-22       Impact factor: 4.411

6.  Artificial intelligence analysis to explore synchronize exercise, cobalamin, and magnesium as new actors to therapeutic of migraine symptoms: a randomized, placebo-controlled trial.

Authors:  Hanie Matin; Farzaneh Taghian; Ahmad Chitsaz
Journal:  Neurol Sci       Date:  2022-02-03       Impact factor: 3.307

7.  PU.1 Mimic Synthetic Peptides Selectively Bind with GATA-1 and Allow c-Jun PU.1 Binding to Enhance Myelopoiesis.

Authors:  Pawan Kumar Raghav; Gurudutta Gangenahalli
Journal:  Int J Nanomedicine       Date:  2021-06-04

8.  Computational Resources for Bioscience Education.

Authors:  Rajiv K Kar
Journal:  Appl Biochem Biotechnol       Date:  2021-06-08       Impact factor: 2.926

Review 9.  Visual pH Sensors: From a Chemical Perspective to New Bioengineered Materials.

Authors:  Luigi Di Costanzo; Barbara Panunzi
Journal:  Molecules       Date:  2021-05-16       Impact factor: 4.411

10.  IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation.

Authors:  Gábor Erdős; Mátyás Pajkos; Zsuzsanna Dosztányi
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.