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a catalog of biological databases

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Database information

PDB (worldwide protein data bank archive)

General information

Description: Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community. Its members [RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and BMRB (USA)] host data‐deposition sites and mirror the PDB ftp archive.
Year founded: 2013
Last update: 2016-03-09
Version: v1.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
Data object:
Database category:
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Keywords:

Contact information

University/Institution: Rutgers The State University of New Jersey
Address: 174 Frelinghuysen Rd, Piscataway, NJ 08854-8087,USA
City: New Jersey
Province/State:
Country/Region: United States
Contact name (PI/Team): Helen M Berman
Contact email (PI/Helpdesk): info@wwpdb.org

Record metadata

Created on: 2015-06-20
Curated by:
Dong Zou [2018-09-18]
huma shireen [2018-09-04]
Lina Ma [2018-06-05]
Tongkun Guo [2018-01-26]
Hongyan Yin [2016-03-29]
Mengwei Li [2016-02-14]
Hongyan Yin [2015-11-25]
Hongyan Yin [2015-06-26]

Ranking

All databases:
59/4499 (98.711%)
Structure:
8/604 (98.841%)
Raw bio-data:
3/447 (99.553%)
59
Total Rank
2,556
Citations
150.353
z-index

Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Publications

29688351
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. [PMID: 29688351]
Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand Gore, Vladimir Guranovic, Pieter M S Hendrickx, Brian P Hudson, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L Lawson, Yuhe Liang, Lora Mak, Abhik Mukhopadhyay, Buvaneswari Narayanan, Kayoko Nishiyama, Ardan Patwardhan, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica R Sekharan, Chenghua Shao, Oliver S Smart, Lihua Tan, Glen van Ginkel, Huanwang Yang, Marina A Zhuravleva, John L Markley, Haruki Nakamura, Genji Kurisu, Gerard J Kleywegt, Sameer Velankar, Helen M Berman, Stephen K Burley

Database URL: https://www.wwpdb.org/.

Database (Oxford). 2018:2018() | 3 Citations (from Europe PMC, 2019-12-14)
29204945
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. [PMID: 29204945]
Zied Gaieb, Shuai Liu, Symon Gathiaka, Michael Chiu, Huanwang Yang, Chenghua Shao, Victoria A Feher, W Patrick Walters, Bernd Kuhn, Markus G Rudolph, Stephen K Burley, Michael K Gilson, Rommie E Amaro

The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank ( http://www.pdb.org ), and in affinity ranking and scoring of bound ligands.

J Comput Aided Mol Des. 2018:32(1) | 21 Citations (from Europe PMC, 2019-12-14)
28573592
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. [PMID: 28573592]
Stephen K Burley, Helen M Berman, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar

The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

Methods Mol Biol. 2017:1607() | 33 Citations (from Europe PMC, 2019-12-14)
28277502
Data management: A global coalition to sustain core data. [PMID: 28277502]
Warwick P Anderson, null null
Nature. 2017:543(7644) | 9 Citations (from Europe PMC, 2019-12-14)
29174494
Validation of Structures in the Protein Data Bank. [PMID: 29174494]
Swanand Gore, Eduardo Sanz García, Pieter M S Hendrickx, Aleksandras Gutmanas, John D Westbrook, Huanwang Yang, Zukang Feng, Kumaran Baskaran, John M Berrisford, Brian P Hudson, Yasuyo Ikegawa, Naohiro Kobayashi, Catherine L Lawson, Steve Mading, Lora Mak, Abhik Mukhopadhyay, Thomas J Oldfield, Ardan Patwardhan, Ezra Peisach, Gaurav Sahni, Monica R Sekharan, Sanchayita Sen, Chenghua Shao, Oliver S Smart, Eldon L Ulrich, Reiko Yamashita, Martha Quesada, Jasmine Y Young, Haruki Nakamura, John L Markley, Helen M Berman, Stephen K Burley, Sameer Velankar, Gerard J Kleywegt

The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.

Structure. 2017:25(12) | 14 Citations (from Europe PMC, 2019-12-14)
28877501
PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. [PMID: 28877501]
Stephen K Burley, Genji Kurisu, John L Markley, Haruki Nakamura, Sameer Velankar, Helen M Berman, Andrej Sali, Torsten Schwede, Jill Trewhella

Burley et al. (leadership of the Worldwide PDB [wwPDB] Partnership [wwpdb.org] and the wwPDB Integrative/Hybrid Methods Task Force) announce public release of a prototype system for depositing integrative/hybrid structural models, PDB-Development (PDB-Dev; https://pdb-dev.wwpdb.org).

Structure. 2017:25(9) | 11 Citations (from Europe PMC, 2019-12-14)
28296894
Impact of genetic variation on three dimensional structure and function of proteins. [PMID: 28296894]
Roshni Bhattacharya, Peter W Rose, Stephen K Burley, Andreas Prli?

The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D) structures of biological macromolecules (proteins, DNA, RNA), all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation.

PLoS One. 2017:12(3) | 2 Citations (from Europe PMC, 2019-12-14)
28190782
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. [PMID: 28190782]
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

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.

Structure. 2017:25(3) | 12 Citations (from Europe PMC, 2019-12-14)
27450113
The archiving and dissemination of biological structure data. [PMID: 27450113]
Helen M Berman, Stephen K Burley, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar

The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day.

Curr Opin Struct Biol. 2016:40() | 13 Citations (from Europe PMC, 2019-12-14)
27050687
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. [PMID: 27050687]
Paul D Adams, Kathleen Aertgeerts, Cary Bauer, Jeffrey A Bell, Helen M Berman, Talapady N Bhat, Jeff M Blaney, Evan Bolton, Gerard Bricogne, David Brown, Stephen K Burley, David A Case, Kirk L Clark, Tom Darden, Paul Emsley, Victoria A Feher, Zukang Feng, Colin R Groom, Seth F Harris, Jorg Hendle, Thomas Holder, Andrzej Joachimiak, Gerard J Kleywegt, Tobias Krojer, Joseph Marcotrigiano, Alan E Mark, John L Markley, Matthew Miller, Wladek Minor, Gaetano T Montelione, Garib Murshudov, Atsushi Nakagawa, Haruki Nakamura, Anthony Nicholls, Marc Nicklaus, Robert T Nolte, Anil K Padyana, Catherine E Peishoff, Susan Pieniazek, Randy J Read, Chenghua Shao, Steven Sheriff, Oliver Smart, Stephen Soisson, John Spurlino, Terry Stouch, Radka Svobodova, Wolfram Tempel, Thomas C Terwilliger, Dale Tronrud, Sameer Velankar, Suzanna C Ward, Gregory L Warren, John D Westbrook, Pamela Williams, Huanwang Yang, Jasmine Young

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ?75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

Structure. 2016:24(4) | 23 Citations (from Europe PMC, 2019-12-14)
25540181
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. [PMID: 25540181]
John D Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young,

The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described.
AVAILABILITY AND IMPLEMENTATION: The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data. The CCD and amino acid variant reference datasets are hosted in the public PDB ftp repository at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz, ftp://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif.gz, and its mirror sites, and can be accessed from http://wwpdb.org.
CONTACT: jwest@rcsb.rutgers.edu.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bioinformatics. 2015:31(8) | 29 Citations (from Europe PMC, 2019-12-14)
26095030
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. [PMID: 26095030]
Andrej Sali, Helen M Berman, Torsten Schwede, Jill Trewhella, Gerard Kleywegt, Stephen K Burley, John Markley, Haruki Nakamura, Paul Adams, Alexandre M J J Bonvin, Wah Chiu, Matteo Dal Peraro, Frank Di Maio, Thomas E Ferrin, Kay Grünewald, Aleksandras Gutmanas, Richard Henderson, Gerhard Hummer, Kenji Iwasaki, Graham Johnson, Catherine L Lawson, Jens Meiler, Marc A Marti-Renom, Gaetano T Montelione, Michael Nilges, Ruth Nussinov, Ardan Patwardhan, Juri Rappsilber, Randy J Read, Helen Saibil, Gunnar F Schröder, Charles D Schwieters, Claus A M Seidel, Dmitri Svergun, Maya Topf, Eldon L Ulrich, Sameer Velankar, John D Westbrook

Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?

Structure. 2015:23(7) | 59 Citations (from Europe PMC, 2019-12-14)
26036565
NMR Exchange Format: a unified and open standard for representation of NMR restraint data. [PMID: 26036565]
Aleksandras Gutmanas, Paul D Adams, Benjamin Bardiaux, Helen M Berman, David A Case, Rasmus H Fogh, Peter Güntert, Pieter M S Hendrickx, Torsten Herrmann, Gerard J Kleywegt, Naohiro Kobayashi, Oliver F Lange, John L Markley, Gaetano T Montelione, Michael Nilges, Timothy J Ragan, Charles D Schwieters, Roberto Tejero, Eldon L Ulrich, Sameer Velankar, Wim F Vranken, Jonathan R Wedell, John Westbrook, David S Wishart, Geerten W Vuister
Nat Struct Mol Biol. 2015:22(6) | 11 Citations (from Europe PMC, 2019-12-14)
25425036
Small molecule annotation for the Protein Data Bank. [PMID: 25425036]
Sanchayita Sen, Jasmine Young, John M Berrisford, Minyu Chen, Matthew J Conroy, Shuchismita Dutta, Luigi Di Costanzo, Guanghua Gao, Sutapa Ghosh, Brian P Hudson, Reiko Igarashi, Yumiko Kengaku, Yuhe Liang, Ezra Peisach, Irina Persikova, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Gaurav Sahni, Junko Sato, Monica Sekharan, Chenghua Shao, Lihua Tan, Marina A Zhuravleva

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

Database (Oxford). 2014:2014() | 9 Citations (from Europe PMC, 2019-12-14)
25286863
Response to On prompt update of literature references in the Protein Data Bank. [PMID: 25286863]
Helen M Berman, Stephen K Burley, Gerard J Kleywegt, Haruki Nakamura, John L Markley

The wwPDB responds to the article On the prompt update of literature references in the Protein Data Bank [Wlodawer (2014), Acta Cryst. D70, 2779].

Acta Crystallogr D Biol Crystallogr. 2014:70(Pt 10) | 1 Citations (from Europe PMC, 2019-12-14)
25062767
The Protein Data Bank archive as an open data resource. [PMID: 25062767]
Helen M Berman, Gerard J Kleywegt, Haruki Nakamura, John L Markley

The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

J Comput Aided Mol Des. 2014:28(10) | 42 Citations (from Europe PMC, 2019-12-14)
24173824
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. [PMID: 24173824]
Shuchismita Dutta, Dimitris Dimitropoulos, Zukang Feng, Irina Persikova, Sanchayita Sen, Chenghua Shao, John Westbrook, Jasmine Young, Marina A Zhuravleva, Gerard J Kleywegt, Helen M Berman

With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide-like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide-like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence. A novel concept called "group" was developed for representing complex peptide-like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide-like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide-like inhibitors and antibiotics accurately and consistently.

Biopolymers. 2014:101(6) | 16 Citations (from Europe PMC, 2019-12-14)
24291661
Chemical annotation of small and peptide-like molecules at the Protein Data Bank. [PMID: 24291661]
Jasmine Y Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, Helen M Berman

Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org.

Database (Oxford). 2013:2013() | 7 Citations (from Europe PMC, 2019-12-14)
24311571
Comment on on the propagation of errors by Jaskolski (2013). [PMID: 24311571]
Helen Berman, Gerard J Kleywegt, Haruki Nakamura, John L Markley
Acta Crystallogr D Biol Crystallogr. 2013:69(Pt 12) | 0 Citations (from Europe PMC, 2019-12-14)
24311570
Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013). [PMID: 24311570]
Helen Berman, Gerard J Kleywegt, Haruki Nakamura, John L Markley
Acta Crystallogr D Biol Crystallogr. 2013:69(Pt 12) | 1 Citations (from Europe PMC, 2019-12-14)
24010707
How community has shaped the Protein Data Bank. [PMID: 24010707]
Helen M Berman, Gerard J Kleywegt, Haruki Nakamura, John L Markley

Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive.

Structure. 2013:21(9) | 8 Citations (from Europe PMC, 2019-12-14)
23023942
The future of the Protein Data Bank. [PMID: 23023942]
Helen M Berman, Gerard J Kleywegt, Haruki Nakamura, John L Markley

The Worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The wwPDB's mission is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Its members [RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and BMRB (USA)] host data-deposition sites and mirror the PDB ftp archive. To support future developments in structural biology, the wwPDB partners are addressing organizational, scientific, and technical challenges.

Biopolymers. 2013:99(3) | 28 Citations (from Europe PMC, 2019-12-14)
23326114
Protein data bank. [PMID: 23326114]
S Parasuraman
J Pharmacol Pharmacother. 2012:3(4) | 11 Citations (from Europe PMC, 2019-12-14)
22404998
The Protein Data Bank at 40: reflecting on the past to prepare for the future. [PMID: 22404998]
Helen M Berman, Gerard J Kleywegt, Haruki Nakamura, John L Markley

A symposium celebrating the 40th anniversary of the Protein Data Bank archive (PDB), organized by the Worldwide Protein Data Bank, was held at Cold Spring Harbor Laboratory (CSHL) October 28-30, 2011. PDB40's distinguished speakers highlighted four decades of innovation in structural biology, from the early era of structural determination to future directions for the field.

Structure. 2012:20(3) | 40 Citations (from Europe PMC, 2019-12-14)
20110969
Safeguarding the integrity of protein archive. [PMID: 20110969]
Helen M Berman, Gerard J Kleywegt, Haruki Nakamura, John L Markley, Stephen K Burley
Nature. 2010:463(7280) | 1 Citations (from Europe PMC, 2019-12-14)
19082769
Data deposition and annotation at the worldwide protein data bank. [PMID: 19082769]
Shuchismita Dutta, Kyle Burkhardt, Jasmine Young, Ganesh J Swaminathan, Takanori Matsuura, Kim Henrick, Haruki Nakamura, Helen M Berman

The Protein Data Bank (PDB) is the repository for three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive is free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and general audiences to understand biological phenomenon at a molecular level. Analysis of this structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

Mol Biotechnol. 2009:42(1) | 67 Citations (from Europe PMC, 2019-12-14)
18288446
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. [PMID: 18288446]
John L Markley, Eldon L Ulrich, Helen M Berman, Kim Henrick, Haruki Nakamura, Hideo Akutsu

We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems.

J Biomol NMR. 2008:40(3) | 47 Citations (from Europe PMC, 2019-12-14)
18645236
Representation of viruses in the remediated PDB archive. [PMID: 18645236]
Catherine L Lawson, Shuchismita Dutta, John D Westbrook, Kim Henrick, Helen M Berman

A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.

Acta Crystallogr D Biol Crystallogr. 2008:D64(Pt 8) | 9 Citations (from Europe PMC, 2019-12-14)
18073189
Remediation of the protein data bank archive. [PMID: 18073189]
Kim Henrick, Zukang Feng, Wolfgang F Bluhm, Dimitris Dimitropoulos, Jurgen F Doreleijers, Shuchismita Dutta, Judith L Flippen-Anderson, John Ionides, Chisa Kamada, Eugene Krissinel, Catherine L Lawson, John L Markley, Haruki Nakamura, Richard Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L Ulrich, Wim Vranken, John Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M Berman

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB-RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)-have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented.

Nucleic Acids Res. 2008:36(Database issue) | 74 Citations (from Europe PMC, 2019-12-14)
18542858
Data deposition and annotation at the worldwide protein data bank. [PMID: 18542858]
Shuchismita Dutta, Kyle Burkhardt, Ganesh J Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, Helen M Berman

The Protein Data Bank (PDB) is the repository for the three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive are free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and lay audiences to understand biological phenomena at a molecular level. Analysis of these structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

Methods Mol Biol. 2008:426() | 8 Citations (from Europe PMC, 2019-12-14)
17142228
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. [PMID: 17142228]
Helen Berman, Kim Henrick, Haruki Nakamura, John L Markley,

The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at http://www.wwpdb.org/ provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.

Nucleic Acids Res. 2007:35(Database issue) | 413 Citations (from Europe PMC, 2019-12-14)
17687352
Realism about PDB. [PMID: 17687352]
Helen M Berman, Kim Henrick, Haruki Nakamura, John Markley, Philip E Bourne, John Westbrook
Nat Biotechnol. 2007:25(8) | 8 Citations (from Europe PMC, 2019-12-14)
18428680
Using the tools and resources of the RCSB protein data bank. [PMID: 18428680]
Shuchismita Dutta, Helen M Berman, Wolfgang F Bluhm

The Protein Data Bank (PDB; http://www.pdb.org) is the world-wide repository for three-dimensional structural data determined using various experimental methods. The options and procedures for searching and downloading structural data from the Research Collaboratory for Structural Bioinformatics (RCSB) PDB are described here, along with tools for assessing the quality of structures. Several types of information are associated with each structure deposition, including atomic coordinates of the structure, experimental data used to solve it, sequences of all macromolecules in the structures, details about the structure solution method, images showing different views of the structure, derived geometric data, and a variety of links to other resources. These data and resources may be used for understanding the function and stability of the molecule and for designing biochemical, genetic, or other experiments. They can also be used for molecular modeling and drug design.

Curr Protoc Bioinformatics. 2007:Chapter 1() | 1 Citations (from Europe PMC, 2019-12-14)
17718923
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. [PMID: 17718923]
Luis A Diago, Persy Morell, Longendri Aguilera, Ernesto Moreno

BACKGROUND: The number of algorithms available to predict ligand-protein interactions is large and ever-increasing. The number of test cases used to validate these methods is usually small and problem dependent. Recently, several databases have been released for further understanding of protein-ligand interactions, having the Protein Data Bank as backend support. Nevertheless, it appears to be difficult to test docking methods on a large variety of complexes. In this paper we report the development of a new database of protein-ligand complexes tailored for testing of docking algorithms.
METHODS: Using a new definition of molecular contact, small ligands contained in the 2005 PDB edition were identified and processed. The database was enriched in molecular properties. In particular, an automated typing of ligand atoms was performed. A filtering procedure was applied to select a non-redundant dataset of complexes. Data mining was performed to obtain information on the frequencies of different types of atomic contacts. Docking simulations were run with the program DOCK.
RESULTS: We compiled a large database of small ligand-protein complexes, enriched with different calculated properties, that currently contains more than 6000 non-redundant structures. As an example to demonstrate the value of the new database, we derived a new set of chemical matching rules to be used in the context of the program DOCK, based on contact frequencies between ligand atoms and points representing the protein surface, and proved their enhanced efficiency with respect to the default set of rules included in that program.
CONCLUSION: The new database constitutes a valuable resource for the development of knowledge-based docking algorithms and for testing docking programs on large sets of protein-ligand complexes. The new chemical matching rules proposed in this work significantly increase the success rate in DOCKing simulations. The database developed in this work is available at http://cimlcsext.cim.sld.cu:8080/screeningbrowser/.

BMC Bioinformatics. 2007:8() | 6 Citations (from Europe PMC, 2019-12-14)
14634627
Announcing the worldwide Protein Data Bank. [PMID: 14634627]
Helen Berman, Kim Henrick, Haruki Nakamura
Nat Struct Biol. 2003:10(12) | 684 Citations (from Europe PMC, 2019-12-14)
12520059
The Protein Data Bank and structural genomics. [PMID: 12520059]
John Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M Berman

The Protein Data Bank (PDB; http://www.pdb.org/) continues to be actively involved in various aspects of the informatics of structural genomics projects--developing and maintaining the Target Registration Database (TargetDB), organizing data dictionaries that will define the specification for the exchange and deposition of data with the structural genomics centers and creating software tools to capture data from standard structure determination applications.

Nucleic Acids Res. 2003:31(1) | 174 Citations (from Europe PMC, 2019-12-14)
12037327
The Protein Data Bank. [PMID: 12037327]
Helen M Berman, Tammy Battistuz, T N Bhat, Wolfgang F Bluhm, Philip E Bourne, Kyle Burkhardt, Zukang Feng, Gary L Gilliland, Lisa Iype, Shri Jain, Phoebe Fagan, Jessica Marvin, David Padilla, Veerasamy Ravichandran, Bohdan Schneider, Narmada Thanki, Helge Weissig, John D Westbrook, Christine Zardecki

The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.

Acta Crystallogr D Biol Crystallogr. 2002:58(Pt 6 No 1) | 661 Citations (from Europe PMC, 2019-12-14)