Literature DB >> 34601771

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

Christine Zardecki1,2, Shuchismita Dutta1,2,3, David S Goodsell1,2,3,4, Robert Lowe1,2, Maria Voigt1,2, Stephen K Burley1,2,3,5,6.   

Abstract

The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic-level three-dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB-101 was launched to support teachers, students, and the general public in PDB archive exploration (pdb101.rcsb.org). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB-101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB-101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year-on-year. In addition, PDB-101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB-101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.
© 2021 The Protein Society.

Entities:  

Keywords:  PDB; Protein Data Bank; education; protein structure and function; structural biology; training

Mesh:

Substances:

Year:  2021        PMID: 34601771      PMCID: PMC8740840          DOI: 10.1002/pro.4200

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


  47 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Announcing the worldwide Protein Data Bank.

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

3.  A course-based undergraduate research experience investigating the consequences of nonconserved mutations in lactate dehydrogenase.

Authors:  Allan Ayella; Moriah R Beck
Journal:  Biochem Mol Biol Educ       Date:  2018-03-07       Impact factor: 1.160

Review 4.  Impact of the Protein Data Bank on antineoplastic approvals.

Authors:  John D Westbrook; Rose Soskind; Brian P Hudson; Stephen K Burley
Journal:  Drug Discov Today       Date:  2020-02-14       Impact factor: 7.851

Review 5.  How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals.

Authors:  John D Westbrook; Stephen K Burley
Journal:  Structure       Date:  2018-12-27       Impact factor: 5.006

Review 6.  Seeing the PDB.

Authors:  Jane S Richardson; David C Richardson; David S Goodsell
Journal:  J Biol Chem       Date:  2021-05-04       Impact factor: 5.157

7.  New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).

Authors:  Akira R Kinjo; Gert-Jan Bekker; Hiroshi Wako; Shigeru Endo; Yuko Tsuchiya; Hiromu Sato; Hafumi Nishi; Kengo Kinoshita; Hirofumi Suzuki; Takeshi Kawabata; Masashi Yokochi; Takeshi Iwata; Naohiro Kobayashi; Toshimichi Fujiwara; Genji Kurisu; Haruki Nakamura
Journal:  Protein Sci       Date:  2017-09-18       Impact factor: 6.725

8.  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

9.  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

10.  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.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Cole H Christie; Kenneth Dalenberg; Luigi Di Costanzo; Jose M Duarte; Shuchismita Dutta; Zukang Feng; Sai Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranović; Dmytro Guzenko; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Harry Namkoong; Ezra Peisach; Irina Persikova; Chris Randle; Alexander Rose; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Yi-Ping Tao; Maria Voigt; John D Westbrook; Jasmine Y Young; Christine Zardecki; Marina Zhuravleva
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

View more
  9 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.  Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.

Authors:  Andrew Keller; Anna A Bakhtina; Juan D Chavez; James E Bruce
Journal:  J Proteome Res       Date:  2022-05-20       Impact factor: 5.370

3.  Network Pharmacology and Bioinformatics Analyses Identify Intersection Genes of Vitamin D3 and COVID-19 as Potential Therapeutic Targets.

Authors:  Shanglin Wang; Huayu Gao; Xiaoru Wang; Xiaoli Ma; Lulu Zhang; Yuanxin Xing; Yanfei Jia; Yunshan Wang
Journal:  Front Pharmacol       Date:  2022-04-28       Impact factor: 5.988

4.  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

5.  Profile of Myracrodruon urundeuva Volatile Compounds Ease of Extraction and Biodegradability and In Silico Evaluation of Their Interactions with COX-1 and iNOS.

Authors:  Yuri G Figueiredo; Eduardo A Corrêa; Afonso H de Oliveira Junior; Ana C D C Mazzinghy; Henrique D O P Mendonça; Yan J G Lobo; Yesenia M García; Marcelo A D S Gouvêia; Ana C C F F de Paula; Rodinei Augusti; Luisa D C B Reina; Carlos H da Silveira; Leonardo H F de Lima; Júlio O F Melo
Journal:  Molecules       Date:  2022-03-01       Impact factor: 4.411

6.  Evaluation of Current Methods to Detect Cellular Leucine-Rich Repeat Kinase 2 (LRRK2) Kinase Activity.

Authors:  Belén Fernández; Vinita G Chittoor-Vinod; Jillian H Kluss; Kaela Kelly; Nicole Bryant; An Phu Tran Nguyen; Syed A Bukhari; Nathan Smith; Antonio Jesús Lara Ordóñez; Elena Fdez; Marie-Christine Chartier-Harlin; Thomas J Montine; Mark A Wilson; Darren J Moore; Andrew B West; Mark R Cookson; R Jeremy Nichols; Sabine Hilfiker
Journal:  J Parkinsons Dis       Date:  2022       Impact factor: 5.520

7.  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

8.  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

9.  Molecular explorations of cancer biology and therapeutics at PDB-101.

Authors:  David S Goodsell; Shuchismita Dutta; Maria Voigt; Christine Zardecki; Stephen K Burley
Journal:  Oncogene       Date:  2022-08-10       Impact factor: 8.756

  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.