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Impact of the Protein Data Bank Across Scientific Disciplines
2020
Data Science Journal
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Feng et al: Impact of the Protein Data Bank Across Scientific Disciplines Art. 25, page 5 of 14
Figure 2 : 2 Figure 2: Top subject categories for publications citing the top-cited PDB structures. ...
Feng et al: Impact of the Protein Data Bank Across Scientific Disciplines Art. 25, page 7 of 14 These structures represent important targets for drug development, and thus are often used to test new structure-based ...
Zukang Feng and Natalie Verdiguel contributed to the design and analysis of the data set and drafted the manuscript. John Westbrook performed the initial citation analysis. ...
doi:10.5334/dsj-2020-025
fatcat:2ahclmqdmbaddmvhr6sj4nonma
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank
2014
Biopolymers
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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 peptidelike inhibitor and antibiotic molecules so that they can be easily
doi:10.1002/bip.22434
pmid:24173824
pmcid:PMC3992913
fatcat:fsy4z23qcfgnvjj2jpn3stgwta
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... fied and analyzed. Peptide-like inhibi-tors 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.
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
2004
Acta Crystallographica Section D: Biological Crystallography
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., 1993) and NUCHECK (Feng et al., 1998) are also produced. ...
doi:10.1107/s0907444904019419
pmid:15388930
fatcat:uuhfm7tfu5auljt24aifx3bd6e
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education
2017
Protein Science
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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
doi:10.1002/pro.3331
pmid:29067736
pmcid:PMC5734314
fatcat:7jdrdkkw6ffffeu2xpsqp3le4i
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... ged 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.
Chemical annotation of small and peptide-like molecules at the Protein Data Bank
2013
Database: The Journal of Biological Databases and Curation
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The Protein Data Bank
2002
Acta Crystallographica Section D: Biological Crystallography
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ADIT is complemented by MAXIT (MAcromolecular EXchange Input Tool; Feng, Hsieh et al., 1998) , a program that performs many of the data-processing tasks and checks. ...
In addition to the summary report letter, the server also provides output from PROCHECK (Laskowski et al., 1993) , NUCheck (Feng, Westbrook et al., 1998) and SFCHECK (Vaguine et al., 1999) . ...
doi:10.1107/s0907444902003451
pmid:12037327
fatcat:satbdpl4a5c2jk7uo42ovv2dgm
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
2014
Computer applications in the biosciences : CABIOS
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The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank 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.
doi:10.1093/bioinformatics/btu789
pmid:25540181
pmcid:PMC4393513
fatcat:k6buqviz3rcuhclavmpmzn233u
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... he 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 data sets are hosted in the public PDB ftp repository at
The life and times of the PDB format – looking towards the future with mmCIF
2021
Acta Crystallographica Section A: Foundations and Advances
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OneDep: unified wwPDB system for deposition, biocuration and validation of macromolecular structures in the PDB archive
2017
Acta Crystallographica Section A: Foundations and Advances
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The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes. Over the past decade, the size and complexity of macromolecules and their complexes with small molecules deposited to the PDB have increased significantly. The PDB archive now holds more than 125,000 experimentally determined structures of biological macromolecules, which are all publicly accessible without restriction. These structures provide essential
doi:10.1107/s0108767317099536
fatcat:ml7nsvdj4nfsxhbs4evta3vgga
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... information to a large, diverse user community worldwide. There are more than 590 millions data file downloads from the PDB archive and more than 1 million unique IP addresses access the archive every year. The worldwide PDB (wwPDB) has developed a global unified system, called OneDep, for deposition, biocuration, and validation of macromolecular structures to the PDB to 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 across all three archives, while supporting growth in the number of depositions and their complexity. In this poster, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide performance assessments. wwPDB members are RCSB PDB (
RCSB Protein Data Bank: sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education
2018
Acta Crystallographica Section A: Foundations and Advances
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T he Protein Data Bank (PDB) was established in 1971 as the first open-access digital data resource in biology. Beginning with only seven protein structures, the PDB archive has ballooned to >138,000 structures of proteins, DNA, and RNA (totaling >1 billion atoms). Today, the PDB is universally regarded as a core data science resource of fundamental importance to the wider lifescience community and long-term preservation of machine-readable biological data. PDB structures are the molecules of
doi:10.1107/s0108767318098811
fatcat:wrqm2gm6wzhl3olcu4323oybtu
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... fe. Knowledge of 3D structures (shapes) of biomolecules, how they evolve with time, and how they function in nature is essential for understanding critical areas of science. PDB data impacts basic and applied research on health and disease of humans, animals, and plants; production of food and energy; and other research pertaining to global prosperity and environmental sustainability. Structure data are also important to biopharmaceutical and biotechnology companies, accelerating data-driven discovery of new drugs, materials, and devices. Today, powerful pulsed X-ray facilities, cryogenic electron microscopes, and new integrative/hybrid (I/H) methods for structure determination are accelerating biomedical research with functional insights into ever more complex biological systems at the atomic level. Cryo-electron tomography even allows study of molecular machines "caught in the act" inside frozen cells. The PDB is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). RCSB PDB (RCSB.org) operates the US wwPDB data center, and makes PDB data available at no charge and without limitations. Studies of website usage, bibliometrics, and economics demonstrate the powerful impact of the PDB data on basic and applied research, clinical medicine, education, and the economy. During calendar 2017, ~680 million structure data files were downloaded by Data Consumers worldwide. During this same period, RCSB PDB processed >6,200 new atomic level biomolecular structures plus experimental data and metadata coming submitted by Data Depositors in the Americas and Oceania. More than >1 million RCSB.org users were served with PDB data integrated with ~40 external resources providing rich structural views of fundamental biology, biomedicine, and energy sciences. Access to PDB data contribute to patent applications, drug discovery and development, publication of scientific studies, innovations that can lead to new product development and company formation, and STEM education. RCSB PDB is funded by the NSF (DBI-1338415), NIH, and DOE.
Outcome of the First Electron Microscopy Validation Task Force Meeting
2012
Structure
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RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
2018
Nucleic Acids Research
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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
doi:10.1093/nar/gky1004
pmid:30357411
pmcid:PMC6324064
fatcat:clctmqo6ujaifm7s27vk3s2h7i
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... llography, 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.'
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
2019
Acta Crystallographica Section D: Structural Biology
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Page 6570 of Mathematical Reviews Vol. , Issue 97J
[page]
1997
Mathematical Reviews
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See Zheng, Quan Shui Zheng, Quan Shui 73024,73057 Ss See Zheng, Xiao Gu Zheng, Xiao Gu Zheng, Yu Zheng, Zukang Zhidkov, P. E. __._* 5 Serene reer Zhong, Huaijie
Zhong, Ning! ...
REESE See Zhang, Jun* SE dnaicahes bxcncsoxsseceneasth 73076 Zhang, Ji Feng
Zhang, Jian-zu
Zhang, Jing-Zhong
Zhang, Jun*
Zhang, Kaizhong
Zhang, Lin*
Zhang, Pei Xuan
Zhang, Pu! ...
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
2017
Structure
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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
doi:10.1016/j.str.2017.01.004
pmid:28190782
pmcid:PMC5360273
fatcat:okamctypwvdrxfomgjio4rsvma
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... tion 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.
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