Literature DB >> 33984281

Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.

Stephen K Burley1, Helen M Berman2.   

Abstract

The Protein Data Bank (PDB) was established in 1971 to archive three-dimensional (3D) structures of biological macromolecules as a public good. Fifty years later, the PDB is providing millions of data consumers around the world with open access to more than 175,000 experimentally determined structures of proteins and nucleic acids (DNA, RNA) and their complexes with one another and small-molecule ligands. PDB data users are working, teaching, and learning in fundamental biology, biomedicine, bioengineering, biotechnology, and energy sciences. They also represent the fields of agriculture, chemistry, physics and materials science, mathematics, statistics, computer science, and zoology, and even the social sciences. The enormous wealth of 3D structure data stored in the PDB has underpinned significant advances in our understanding of protein architecture, culminating in recent breakthroughs in protein structure prediction accelerated by artificial intelligence approaches and deep or machine learning methods.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  CAMEO; CAPRI; CASP; FAIR principles; PDB50; Protein Data Bank; artificial intelligence; de novo protein structure prediction; drug design data resource; machine learning; open-access biodata resource; protein structure; structural biology; structure-guided drug discovery

Mesh:

Substances:

Year:  2021        PMID: 33984281      PMCID: PMC8178243          DOI: 10.1016/j.str.2021.04.010

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.871


  48 in total

1.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

2.  The Protein Data Bank: a historical perspective.

Authors:  Helen M Berman
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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.  Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive.

Authors:  Chenghua Shao; Huanwang Yang; John D Westbrook; Jasmine Y Young; Christine Zardecki; Stephen K Burley
Journal:  Structure       Date:  2017-02-16       Impact factor: 5.006

5.  Structure of the human class I histocompatibility antigen, HLA-A2.

Authors:  P J Bjorkman; M A Saper; B Samraoui; W S Bennett; J L Strominger; D C Wiley
Journal:  Nature       Date:  1987 Oct 8-14       Impact factor: 49.962

Review 6.  The promise and the challenges of cryo-electron tomography.

Authors:  Martin Turk; Wolfgang Baumeister
Journal:  FEBS Lett       Date:  2020-10-23       Impact factor: 4.124

7.  Improved protein structure prediction using potentials from deep learning.

Authors:  Andrew W Senior; Richard Evans; John Jumper; James Kirkpatrick; Laurent Sifre; Tim Green; Chongli Qin; Augustin Žídek; Alexander W R Nelson; Alex Bridgland; Hugo Penedones; Stig Petersen; Karen Simonyan; Steve Crossan; Pushmeet Kohli; David T Jones; David Silver; Koray Kavukcuoglu; Demis Hassabis
Journal:  Nature       Date:  2020-01-15       Impact factor: 49.962

Review 8.  Blinatumomab, a bispecific B-cell and T-cell engaging antibody, in the treatment of B-cell malignancies.

Authors:  Richard Burt; Dana Warcel; Adele K Fielding
Journal:  Hum Vaccin Immunother       Date:  2018-11-20       Impact factor: 3.452

Review 9.  Melanoma biology and new targeted therapy.

Authors:  Vanessa Gray-Schopfer; Claudia Wellbrock; Richard Marais
Journal:  Nature       Date:  2007-02-22       Impact factor: 49.962

10.  Integrative illustration for coronavirus outreach.

Authors:  David S Goodsell; Maria Voigt; Christine Zardecki; Stephen K Burley
Journal:  PLoS Biol       Date:  2020-08-06       Impact factor: 8.029

View more
  4 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.  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

3.  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

4.  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
  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.