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Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive

Chenghua Shao, Huanwang Yang, John D. Westbrook, Jasmine Y. Young, Christine Zardecki, Stephen K. Burley
2017 Structure  
A73, a187-a188 Chenghua Shao RCSB PDB; Rutgers, The State University of New Jersey Huanwang Yang RCSB PDB; Rutgers, The State University of New Jersey John D Westbrook RCSB PDB; Rutgers, The State University  ... 
doi:10.1016/j.str.2017.01.013 pmid:28216043 pmcid:PMC7182075 fatcat:kojf7bk2ijcvlfkkeg5m2vp56m

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Chenghua Shao, Zonghong Liu, Huanwang Yang, Sijian Wang, Stephen K. Burley
2018 Scientific Data  
Outlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for
more » ... t assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.
doi:10.1038/sdata.2018.293 fatcat:qnn7mj7weravhpmw63mtfqd3iu

DCC: a Swiss army knife for structure factor analysis and validation

Huanwang Yang, Ezra Peisach, John D. Westbrook, Jasmine Young, Helen M. Berman, Stephen K. Burley
2016 Journal of Applied Crystallography  
Cryst. (2016). 49, 1081-1084 Huanwang Yang et al. DCC 1083 J. Appl. Cryst.(2016). 49, 1081-1084  ... 
doi:10.1107/s1600576716004428 pmid:27275151 pmcid:PMC4886994 fatcat:ii7y57js6nhebbgjped2ckyhka

Impact of external odor on self-grooming of lesser flat-headed bats, Tylonycteris pachypus

Jie Liang, Jian Yang, Huanwang Xie, Xingwen Peng, Xiangyang He, Yunxiao Sun, Libiao Zhang
2019 Ecology and Evolution  
Jian Yang and Xiangyang He performed the experiments. Jie Liang, Xingwen Peng, and Yunxiao Sun analyzed the data, Libiao Zhang, Jie Liang and Huanwang Xie wrote the manuscript.  ...  a) control group (CG), (b) conspecifics from different colonies in the same forest roost (DCG), (c) conspecifics from different roosts (DRG), (d) AUTH O R CO NTR I B UTI O N S Libiao Zhang and Jian Yang  ... 
doi:10.1002/ece3.5377 pmid:31380075 pmcid:PMC6662324 fatcat:rdxw2zc7mrgwhhvk7bpaaihsnm

Multivariate analyses of quality metrics for crystal structures in the PDB archive

Chenghua Shao, Huanwang Yang, John D. Westbrook, Jasmine Young, Christine Zardecki, Stephen K. Burley
2017 Acta Crystallographica Section A: Foundations and Advances  
A73, a187-a188 Chenghua Shao RCSB PDB; Rutgers, The State University of New Jersey Huanwang Yang RCSB PDB; Rutgers, The State University of New Jersey John D Westbrook RCSB PDB; Rutgers, The State University  ... 
doi:10.1107/s0108767317098142 fatcat:lhfv6ht5pbbuhmitc2djjzd63q

Trendspotting in the Protein Data Bank

Helen M. Berman, Buvaneswari Coimbatore Narayanan, Luigi Di Costanzo, Shuchismita Dutta, Sutapa Ghosh, Brian P. Hudson, Catherine L. Lawson, Ezra Peisach, Andreas Prlić, Peter W. Rose, Chenghua Shao, Huanwang Yang (+2 others)
2013 FEBS Letters  
The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85 000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.
doi:10.1016/j.febslet.2012.12.029 pmid:23337870 pmcid:PMC4068610 fatcat:pc6muagsrzh6lcqjm4ewkct5sa

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  
D60, 1833±1839 Yang et al. Protein Data Bank deposition 1835 Figure 3 research papers 1834 papers Yang et al. Protein Data Bank deposition Acta Cryst. (2004).  ... 
doi:10.1107/s0907444904019419 pmid:15388930 fatcat:uuhfm7tfu5auljt24aifx3bd6e

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

Symon Gathiaka, Shuai Liu, Michael Chiu, Huanwang Yang, Jeanne A. Stuckey, You Na Kang, Jim Delproposto, Ginger Kubish, James B. Dunbar, Heather A. Carlson, Stephen K. Burley, W. Patrick Walters (+3 others)
2016 Journal of Computer-Aided Molecular Design  
The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (i) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (ii) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural
more » ... and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand-protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy.
doi:10.1007/s10822-016-9946-8 pmid:27696240 pmcid:PMC5562487 fatcat:akvv3ttra5d65msjn62jwntsqm

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

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  
The DCC program (Yang et al., 2016) is-used to assess whether or not Depositor-reported values for R-factor and R-free can be reproduced.  ...  Popular structure refinement packages already export PDBx/mmCIF formatted files, and the pdb_extract tool (Yang et al., 2004) , can be used to prepare valid PDBx/mmCIF formatted files from legacy PDB  ... 
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

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 (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Citation details: Young,J.Y., Westbrook,J.D., Feng,Z. et al. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The V C The Author(s) worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability,
more » ... ccessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a highquality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

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 (+45 others)
2016 Structure  
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
more » ... 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 macromoleculeligand 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.
doi:10.1016/j.str.2016.02.017 pmid:27050687 pmcid:PMC5070601 fatcat:4qqem23wangqlnumkg2tcxe4ti

mmCIF applications at the RCSB Protein Data Bank

Z. Feng, H. M. Berman, H. Yang, J. D. Westbrook
2005 Acta Crystallographica Section A Foundations of Crystallography  
Berman, Huanwang Yang, John D. Westbrook, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey. Email: jwest@rcsb.rutgers.edu  ... 
doi:10.1107/s0108767305094584 fatcat:66orlhwcdvf7vmzs75fw4ngaqa

mmCIF and dictionary driven software with the MSD database production pipeline

K. Henrick, S. Valenkar, H. Boutselakis, A. Hussain, J. Ionides, A. Kapopoulou, P. Keller, R. Newman, J. Pineda, A. Suarez, J. Swaminathan, J. Tate
2005 Acta Crystallographica Section A Foundations of Crystallography  
Berman, Huanwang Yang, John D. Westbrook, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey. Email: jwest@rcsb.rutgers.edu  ... 
doi:10.1107/s0108767305094596 fatcat:kruktikirzbghdah7o5hyyiu4q
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