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Impact of the Protein Data Bank Across Scientific Disciplines

Zukang Feng, Natalie Verdiguel, Luigi Di Costanzo, David S. Goodsell, John D. Westbrook, Stephen K. Burley, Christine Zardecki
2020 Data Science Journal  
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

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
2014 Biopolymers  
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
more » ... 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.
doi:10.1002/bip.22434 pmid:24173824 pmcid:PMC3992913 fatcat:fsy4z23qcfgnvjj2jpn3stgwta

Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank

Huanwang Yang, Vladimir Guranovic, Shuchismita Dutta, Zukang Feng, Helen M. Berman, John D. Westbrook
2004 Acta Crystallographica Section D: Biological Crystallography  
., 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

Stephen K. Burley, Helen M. Berman, Cole Christie, Jose M. Duarte, Zukang Feng, John Westbrook, Jasmine Young, Christine Zardecki
2017 Protein Science  
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
more » ... 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.
doi:10.1002/pro.3331 pmid:29067736 pmcid:PMC5734314 fatcat:7jdrdkkw6ffffeu2xpsqp3le4i

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

Jasmine Y. Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, Helen M. Berman
2013 Database: The Journal of Biological Databases and Curation  
doi:10.1093/database/bat079 pmid:24291661 pmcid:PMC3843158 fatcat:fcw46qnbfbhe5cjpxb7x7etiea

The Protein Data Bank

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 (+7 others)
2002 Acta Crystallographica Section D: Biological Crystallography  
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

John D. Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young
2014 Computer applications in the biosciences : CABIOS  
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.
more » ... 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
doi:10.1093/bioinformatics/btu789 pmid:25540181 pmcid:PMC4393513 fatcat:k6buqviz3rcuhclavmpmzn233u

The life and times of the PDB format – looking towards the future with mmCIF

Gregg Crichlow, Catherine Lawson, John Westbrook, Stephen Burley, Sanja Abbott, Kumaran Baskaran, John Berrisford, Zukang Feng, Yasuyo Ikegawa, Masashi Yokochi, Jasmine Y. Young, Jeffrey Hoch (+1 others)
2021 Acta Crystallographica Section A: Foundations and Advances  
doi:10.1107/s0108767321098068 fatcat:bjkhzjzsm5hojhv6ovbgaziowa

OneDep: unified wwPDB system for deposition, biocuration and validation of macromolecular structures in the PDB archive

Jasmine Y. Young, John Westbrook, Zukang Feng, wwPDB Biocuration Team, wwPDB Onedep Team, John Markley, Haruki Nakamura, Sameer Velankar, Stephen K. Burley
2017 Acta Crystallographica Section A: Foundations and Advances  
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
more » ... 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 (
doi:10.1107/s0108767317099536 fatcat:ml7nsvdj4nfsxhbs4evta3vgga

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

Christine Zardecki, Helen M. Berman, Cole Christie, Jose M. Duarte, Zukang Feng, John Westbrook, Jasmine Young, Stephen K. Burley
2018 Acta Crystallographica Section A: Foundations and Advances  
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
more » ... 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.
doi:10.1107/s0108767318098811 fatcat:wrqm2gm6wzhl3olcu4323oybtu

Outcome of the First Electron Microscopy Validation Task Force Meeting

Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke (+16 others)
2012 Structure  
doi:10.1016/j.str.2011.12.014 pmid:22325770 pmcid:PMC3328769 fatcat:y57hbr2qijg33bhqo3bp5qqqbi

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh (+28 others)
2018 Nucleic Acids Research  
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
more » ... 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.'
doi:10.1093/nar/gky1004 pmid:30357411 pmcid:PMC6324064 fatcat:clctmqo6ujaifm7s27vk3s2h7i

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, Helen M. Berman, John Berrisford, Gerard Bricogne, David G. Brown, Stephen K. Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas (+23 others)
2019 Acta Crystallographica Section D: Structural Biology  
doi:10.1107/s2059798319004522 pmid:30988261 pmcid:PMC6465986 fatcat:lfqllnbmuzapnc4cv2r4za3ncy

Page 6570 of Mathematical Reviews Vol. , Issue 97J [page]

1997 Mathematical Reviews  
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

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 (+37 others)
2017 Structure  
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
more » ... 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.
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma
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