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Helen M Berman - One of the best experts on this subject based on the ideXlab platform.

  • synergies between the Protein Data Bank and the community
    Nature Structural & Molecular Biology, 2021
    Co-Authors: Helen M Berman
    Abstract:

    The Protein Data Bank (PDB) is a community resource. But how do we define community, and how has it changed over the last 50 years since the PDB was founded? How did the community influence the evolution of the PDB, and how did the PDB influence both the science and the behavior of the community?

  • how the Protein Data Bank changed biology an introduction to the jbc reviews thematic series part 1
    Journal of Biological Chemistry, 2021
    Co-Authors: Helen M Berman, Lila M Gierasch
    Abstract:

    This collection of articles celebrates the 50th anniversary of the Protein Data Bank (PDB), the single global digital archive of biological macromolecular structures. The impact of the PDB is immense; we have invited a number of top researchers in structural biology to illustrate its influence on an array of scientific fields. What emerges is a compelling picture of the synergism between the PDB and the explosive progress witnessed in many scientific areas. Availability of reliable, openly accessible, well-archived structural information has arguably had more impact on cell and molecular biology than even some of the enabling technologies such as PCR. We have seen the science move from a time when structural biologists contributed the lion’s share of the structures to the PDB and for discussion within their community to a time when any effort to achieve in-depth understanding of a biochemical or cell biological question demands an interdisciplinary approach built atop structural underpinnings.

  • how the Protein Data Bank changed biology an introduction to the jbc reviews thematic series part 2
    Journal of Biological Chemistry, 2021
    Co-Authors: Lila M Gierasch, Helen M Berman
    Abstract:

    In part 1 of this remarkable collection, we told you the story of The Protein Data Bank (PDB) (1), which was founded 50 years ago, and we illustrated the breadth of the science contained within it with ten informative review articles. The second half of this collection is a continuation of our celebrations to mark this momentous anniversary. Part 2 provides eight more superb articles describing how the PDB has influenced biology over the course of the last half-century and how biology has fueled the deposition of impactful structures in the PDB. Here are some brief synopses of the articles you will enjoy in part 2!

  • announcing mandatory submission of pdbx mmcif format files for crystallographic depositions to the Protein Data Bank pdb
    Acta crystallographica. Section D Structural biology, 2019
    Co-Authors: Helen M Berman, Stephen K. Burley, Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, John M. Berrisford, Gérard Bricogne, David Graham Brown
    Abstract:

    This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).

  • rcsb Protein Data Bank biological macromolecular structures enabling research and education in fundamental biology biomedicine biotechnology and energy
    Nucleic Acids Research, 2019
    Co-Authors: S K Burley, Helen M Berman, Li Chen, Luigi Di Costanzo, Jose M Duarte, Charmi Bhikadiya, Cole H. Christie, Chunxiao Bi, Ken Dalenberg, Shuchismita Dutta
    Abstract:

    : The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US Data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure Data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'

Stephen K. Burley - One of the best experts on this subject based on the ideXlab platform.

  • rcsb Protein Data Bank celebrating 50 years of the pdb with new tools for understanding and visualizing biological macromolecules in 3d
    Protein Science, 2021
    Co-Authors: Stephen K. Burley, Zukang Feng, Li Chen, Shuchismita Dutta, Jose M Duarte, Charmi Bhikadiya, Sebastian Bittrich, Gregg V Crichlow, Maryam Fayazi, Justin W Flatt
    Abstract:

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) Data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US Data center for the global PDB archive housing biomolecular structure Data. RCSB PDB is also responsible for the security of PDB Data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure Data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB Data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB Data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of Data standards and Data remediation in effective management of the archive and facile integration with more than 50 external Data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

  • modernized uniform representation of carbohydrate molecules in the Protein Data Bank
    Glycobiology, 2021
    Co-Authors: Chenghua Shao, Yasuyo Ikegawa, Zukang Feng, John D Westbrook, Sameer Velankar, Stephen K. Burley, Ezra Peisach, John M. Berrisford, Genji Kurisu, Jasmine Young
    Abstract:

    Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for Data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable Data representation for carbohydrates occurring in the PDB structures and the corresponding reference Data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File Data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in Proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoProteins.

  • the Protein Data Bank archive
    Methods of Molecular Biology, 2021
    Co-Authors: Sameer Velankar, Stephen K. Burley, Genji Kurisu, Jeffrey C Hoch, John L Markley
    Abstract:

    Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure Data. Established in 1971 as the first open access Data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-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 PDB archive currently includes ~175,000 entries. The wwPDB has established a number of task forces and working groups that bring together experts form the community who provide recommendations on improving Data standards and Data validation for improving Data quality and integrity. The wwPDB members continue to develop the joint deposition, biocuration, and validation system (OneDep) to improve Data quality and accommodate new Data from emerging techniques such as 3DEM. Each PDB entry contains coordinate model and associated metaData for all experimentally determined atomic structures, experimental Data for the traditional structure determination techniques (X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy), validation reports, and additional information on quaternary structures. The wwPDB partners are committed to following the FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles and have implemented a DOI resolution mechanism that provides access to all the relevant files for a given PDB entry. On average, >250 new entries are added to the archive every week and made available by each wwPDB partner via FTP area. The wwPDB partner sites also develop Data access and analysis tools and make these available via their websites. wwPDB continues to work with experts in the community to establish a federation of archives for archiving structures determined using integrative/hybrid method where multiple experimental techniques are used.

  • rcsb Protein Data Bank 1d tools and services
    Bioinformatics, 2020
    Co-Authors: Joan Segura, John D Westbrook, Stephen K. Burley, Yana Rose, Jose M Duarte
    Abstract:

    MOTIVATION Interoperability between polymer sequences and structural Data is essential for providing a complete picture of Protein and gene features and helping to understand biomolecular function. RESULTS Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI, and the UniProtKB Data resources and visualize integrated Data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional Data over the web. AVAILABILITY https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. SUPPLEMENTARY INFORMATION Supplementary Data are available at Bioinformatics online.

  • Real time structural search of the Protein Data Bank
    PLoS computational biology, 2020
    Co-Authors: Dmytro Guzenko, Stephen K. Burley, Jose M Duarte
    Abstract:

    Detection of Protein structure similarity is a central challenge in structural bioinformatics. Comparisons are usually performed at the polypeptide chain level, however the functional form of a Protein within the cell is often an oligomer. This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval. Traditional methods use atom level information, which can be complicated by the presence of topological permutations within a polypeptide chain and/or subunit rearrangements. These challenges can be overcome by comparing electron density volumes directly. But, brute force alignment of 3D Data is a compute intensive search problem. We developed a 3D Zernike moment normalization procedure to orient electron density volumes and assess similarity with unprecedented speed. Similarity searching with this approach enables real-time retrieval of Proteins/Protein assemblies resembling a target, from PDB or user input, together with resulting alignments (http://shape.rcsb.org).

Haruki Nakamura - One of the best experts on this subject based on the ideXlab platform.

  • Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
    Methods in molecular biology (Clifton N.J.), 2017
    Co-Authors: Stephen K. Burley, Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley, Sameer Velankar
    Abstract:

    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.

  • Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
    Nucleic Acids Research, 2016
    Co-Authors: Akira R. Kinjo, Yasuyo Ikegawa, Gert-jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited Data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of Proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational Database that support the former. To enhance the interoperability of the PDB Data, we have previously developed PDB/RDF, PDB Data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF Data by incorporating various external Data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

  • The Protein Data Bank archive as an open Data resource
    Journal of computer-aided molecular design, 2014
    Co-Authors: Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley
    Abstract:

    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.

  • How Community Has Shaped the Protein Data Bank
    Structure (London England : 1993), 2013
    Co-Authors: Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley
    Abstract:

    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.

  • The future of the Protein Data Bank
    Biopolymers, 2012
    Co-Authors: Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley
    Abstract:

    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.

Zukang Feng - One of the best experts on this subject based on the ideXlab platform.

  • rcsb Protein Data Bank celebrating 50 years of the pdb with new tools for understanding and visualizing biological macromolecules in 3d
    Protein Science, 2021
    Co-Authors: Stephen K. Burley, Zukang Feng, Li Chen, Shuchismita Dutta, Jose M Duarte, Charmi Bhikadiya, Sebastian Bittrich, Gregg V Crichlow, Maryam Fayazi, Justin W Flatt
    Abstract:

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) Data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US Data center for the global PDB archive housing biomolecular structure Data. RCSB PDB is also responsible for the security of PDB Data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure Data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB Data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB Data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of Data standards and Data remediation in effective management of the archive and facile integration with more than 50 external Data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

  • modernized uniform representation of carbohydrate molecules in the Protein Data Bank
    Glycobiology, 2021
    Co-Authors: Chenghua Shao, Yasuyo Ikegawa, Zukang Feng, John D Westbrook, Sameer Velankar, Stephen K. Burley, Ezra Peisach, John M. Berrisford, Genji Kurisu, Jasmine Young
    Abstract:

    Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for Data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable Data representation for carbohydrates occurring in the PDB structures and the corresponding reference Data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File Data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in Proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoProteins.

  • enhanced validation of small molecule ligands and carbohydrates in the Protein Data Bank
    Structure, 2021
    Co-Authors: Zukang Feng, John D Westbrook, Gérard Bricogne, Raul Sala, Oliver S Smart, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F Aokikinoshita, Jeffrey C Hoch
    Abstract:

    Summary The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental Data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery.

  • Impact of the Protein Data Bank across scientific disciplines
    Data Science Journal, 2020
    Co-Authors: Zukang Feng, John D Westbrook, Stephen K. Burley, Luigi Di Costanzo, David S. Goodsell, Natalie Verdiguel, Christine Zardecki
    Abstract:

    The Protein Data Bank archive (PDB) was established in 1971 as the 1st open access digital Data resource for biology and medicine. Today, the PDB contains >160,000 atomic-level, experimentally-determined 3D biomolecular structures. PDB Data are freely and publicly available for download, without restrictions. Each entry contains summary information about the structure and experiment, atomic coordinates, and in most cases, a citation to a corresponding scientific publication. Individually and in bulk, PDB structures can be downloaded and/or analyzed and visualized online using tools at RCSB.org. As such, it is challenging to understand and monitor reuse of Data. Citations of the scientific publications describing PDB structures provide one way of understanding which structures are being used, and in which research areas. Our analysis highlights frequently-cited structures and identifies milestone structures that have demonstrated impact across scientific fields.

  • rcsb Protein Data Bank sustaining a living digital Data resource that enables breakthroughs in scientific research and biomedical education
    Protein Science, 2018
    Co-Authors: Helen M Berman, Zukang Feng, John D Westbrook, Stephen K. Burley, Jasmine Young, Jose M Duarte, Cole H. Christie, Christine Zardecki
    Abstract:

    The Protein Data Bank (PDB) is one of two archival resources for experimental Data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-Data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure Data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental Data and metaData coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB Data integrated with ∼40 external Data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB Data on basic and applied research, clinical medicine, education, and the economy.

John L Markley - One of the best experts on this subject based on the ideXlab platform.

  • the Protein Data Bank archive
    Methods of Molecular Biology, 2021
    Co-Authors: Sameer Velankar, Stephen K. Burley, Genji Kurisu, Jeffrey C Hoch, John L Markley
    Abstract:

    Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure Data. Established in 1971 as the first open access Data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-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 PDB archive currently includes ~175,000 entries. The wwPDB has established a number of task forces and working groups that bring together experts form the community who provide recommendations on improving Data standards and Data validation for improving Data quality and integrity. The wwPDB members continue to develop the joint deposition, biocuration, and validation system (OneDep) to improve Data quality and accommodate new Data from emerging techniques such as 3DEM. Each PDB entry contains coordinate model and associated metaData for all experimentally determined atomic structures, experimental Data for the traditional structure determination techniques (X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy), validation reports, and additional information on quaternary structures. The wwPDB partners are committed to following the FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles and have implemented a DOI resolution mechanism that provides access to all the relevant files for a given PDB entry. On average, >250 new entries are added to the archive every week and made available by each wwPDB partner via FTP area. The wwPDB partner sites also develop Data access and analysis tools and make these available via their websites. wwPDB continues to work with experts in the community to establish a federation of archives for archiving structures determined using integrative/hybrid method where multiple experimental techniques are used.

  • Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
    Methods in molecular biology (Clifton N.J.), 2017
    Co-Authors: Stephen K. Burley, Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley, Sameer Velankar
    Abstract:

    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.

  • The Protein Data Bank archive as an open Data resource
    Journal of computer-aided molecular design, 2014
    Co-Authors: Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley
    Abstract:

    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.

  • How Community Has Shaped the Protein Data Bank
    Structure (London England : 1993), 2013
    Co-Authors: Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley
    Abstract:

    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.

  • The future of the Protein Data Bank
    Biopolymers, 2012
    Co-Authors: Helen M Berman, Haruki Nakamura, Gerard J Kleywegt, John L Markley
    Abstract:

    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.

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