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

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 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 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

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 Integration of open access literature into the RCSB Protein Data Bank using BioLit

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Andreas Prlić ◽  
Marco A Martinez ◽  
Dimitris Dimitropoulos ◽  
Bojan Beran ◽  
Benjamin T Yukich ◽  
...  
Keyword(s):  
Open Access ◽  
Protein Data Bank ◽  
Data Bank

scholarly journals The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

2014 ◽  
Vol 43 (D1) ◽  
pp. D345-D356 ◽  
Author(s):  
Peter W. Rose ◽  
Andreas Prlić ◽  
Chunxiao Bi ◽  
Wolfgang F. Bluhm ◽  
Cole H. Christie ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Applied Research ◽  
Data Bank ◽  
Basic And Applied Research ◽  
Research And Education

scholarly journals Making glycoproteins a little bit sweeter withPDB-REDO

2018 ◽  
Vol 74 (8) ◽  
pp. 463-472 ◽  
Author(s):  
Bart van Beusekom ◽  
Thomas Lütteke ◽  
Robbie P. Joosten
Keyword(s):  
Experimental Data ◽  
Amino Acid ◽  
Protein Data Bank ◽  
Model Building ◽  
Data Bank ◽  
Structure Model ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
High Quality ◽  
Glycoprotein Structure

Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement byPDB-REDOof 8114 glycoprotein structure models from the Protein Data Bank are analyzed. The positive aspects of 3620 reannotations and subsequent refinement, as well as the remaining challenges to obtaining consistently high-quality carbohydrate models, are discussed.

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