scholarly journals The data universe of structural biology

IUCrJ ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 630-638 ◽  
Author(s):  
Helen M. Berman ◽  
Brinda Vallat ◽  
Catherine L. Lawson
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Data Bank ◽  
Small Data ◽  
Complex Structures ◽  
Data Resource ◽  
History Of

The Protein Data Bank (PDB) has grown from a small data resource for crystallographers to a worldwide resource serving structural biology. The history of the growth of the PDB and the role that the community has played in developing standards and policies are described. This article also illustrates how other biophysics communities are collaborating with the worldwide PDB to create a network of interoperating data resources. This network will expand the capabilities of structural biology and enable the determination and archiving of increasingly complex structures.

scholarly journals The history of the PDB as a public resource for enabling science

2014 ◽  
Vol 70 (a1) ◽  
pp. C934-C934
Author(s):  
Helen Berman
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Scientific Community ◽  
Access Point ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Science Technology ◽  
Public Resource ◽  
History Of ◽  
Online Access

As the crystal structures of biological macromolecules were being determined, a new field of structural biology was born. Inspired by these new structures, the scientific community worked to establish a home to archive and share the data emerging from these experiments. The Protein Data Bank (PDB) was established in 1971 with seven structures. The PDB provides a repository for scientists who generate the data, and an access point for researchers and students to find the information needed to drive additional studies. Today, the PDB contains and supports online access to ~100,000 biomacromolecules that help researchers understand aspects of biology, including medicine, agriculture, and biological energy. The ways in which the interrelationships among science, technology, and community have driven the evolution of the PDB resource for more than forty years will be discussed. The PDB archive is managed by the Worldwide Protein Data Bank (wwpdb.org), whose members are the RCSB PDB, PDBe, PDBj and BMRB.

scholarly journals Crystallographic raw data, education and refereeing

2016 ◽  
Vol 62 (3) ◽  
pp. 257-261
Author(s):  
John R. Helliwell
Keyword(s):  
Experimental Data ◽  
Protein Data Bank ◽  
Structural Biology ◽  
Diffraction Data ◽  
Review Process ◽  
Data Bank ◽  
The Impact ◽  
And Training ◽  
Scientific Achievements ◽  
Future Plans

This article provides an overview of the preservation of raw diffraction data, then addresses the impact on future plans in the education and training of our community with respect to raw diffraction data and its potential reuse, and, thirdly presents the issue of referee access to the underpinning diffraction data and coordinates, as well as the Protein Data Bank Validation Report, in the review process of structural biology articles submitted for publication. Overall I pay tribute to the scientific achievements of Alex Wlodawer, who is also an ardent advocate of the importance of experimental data

scholarly journals RCSB Protein Data Bank: Sustaining A Living Digital Data Resource That Enables Breakthroughs In Scientific Research And Biomedical Education

2018 ◽  
Vol 32 (S1) ◽  
Author(s):  
Stephen K. Burley ◽  
Helen M. Berman ◽  
Cole Christie ◽  
Jose M. Duarte ◽  
Zukang Feng ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Scientific Research ◽  
Data Bank ◽  
Digital Data ◽  
Data Resource ◽  
Biomedical Education

scholarly journals Educational Resources for Structural Biology at the RCSB Protein Data Bank

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Shuchismita Dutta ◽  
Jeff Milton ◽  
Christine Zardecki ◽  
Helen M Berman
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Data Bank ◽  
Educational Resources

scholarly journals RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

2017 ◽  
Vol 27 (1) ◽  
pp. 316-330 ◽  
Author(s):  
Stephen K. Burley ◽  
Helen M. Berman ◽  
Cole Christie ◽  
Jose M. Duarte ◽  
Zukang Feng ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Scientific Research ◽  
Data Bank ◽  
Digital Data ◽  
Data Resource ◽  
Biomedical Education

MLDB: macromolecule ligand database

2009 ◽  
Vol 43 (1) ◽  
pp. 200-202 ◽  
Author(s):  
S. E. Saravanan ◽  
R. Karthi ◽  
K. Sathish ◽  
K. Kokila ◽  
R. Sabarinathan ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Scientific Community ◽  
Three Dimensional ◽  
Data Bank

MLDB (macromolecule ligand database) is a knowledgebase containing ligands co-crystallized with the three-dimensional structures available in the Protein Data Bank. The proposed knowledgebase serves as an open resource for the analysis and visualization of all ligands and their interactions with macromolecular structures. MLDB can be used to search ligands, and their interactions can be visualized both in text and graphical formats. MLDB will be updated at regular intervals (weekly) with automated Perl scripts. The knowledgebase is intended to serve the scientific community working in the areas of molecular and structural biology. It is available free to users around the clock and can be accessed at http://dicsoft2.physics.iisc.ernet.in/mldb/.

scholarly journals The Protein Data Bank archive as an open data resource

2014 ◽  
Vol 28 (10) ◽  
pp. 1009-1014 ◽  
Author(s):  
Helen M. Berman ◽  
Gerard J. Kleywegt ◽  
Haruki Nakamura ◽  
John L. Markley
Keyword(s):  
Protein Data Bank ◽  
Open Data ◽  
Data Bank ◽  
Data Resource

scholarly journals Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Database ◽  
2018 ◽  
Vol 2018 ◽  
Author(s):  
Jasmine Y Young ◽  
John D Westbrook ◽  
Zukang Feng ◽  
Ezra Peisach ◽  
Irina Persikova ◽  
...  
Keyword(s):  
Open Access ◽  
Protein Data Bank ◽  
Structural Biology ◽  
Data Bank ◽  
High Quality
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