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Title: Validation of Structures in the Protein Data Bank

Abstract

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.

Authors:
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Publication Date:
Research Org.:
Rutgers Univ., Piscataway, NJ (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1410138
Alternate Identifier(s):
OSTI ID: 1623723
Grant/Contract Number:  
DBI-1338415; FG02-00ER41132
Resource Type:
Published Article
Journal Name:
Structure
Additional Journal Information:
Journal Name: Structure Journal Volume: 25 Journal Issue: 12; Journal ID: ISSN 0969-2126
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biophysics; Cell Biology

Citation Formats

Gore, Swanand, Sanz García, Eduardo, Hendrickx, Pieter M. S., Gutmanas, Aleksandras, Westbrook, John D., Yang, Huanwang, Feng, Zukang, Baskaran, Kumaran, Berrisford, John M., Hudson, Brian P., Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Mading, Steve, Mak, Lora, Mukhopadhyay, Abhik, Oldfield, Thomas J., Patwardhan, Ardan, Peisach, Ezra, Sahni, Gaurav, Sekharan, Monica R., Sen, Sanchayita, Shao, Chenghua, Smart, Oliver S., Ulrich, Eldon L., Yamashita, Reiko, Quesada, Martha, Young, Jasmine Y., Nakamura, Haruki, Markley, John L., Berman, Helen M., Burley, Stephen K., Velankar, Sameer, and Kleywegt, Gerard J.. Validation of Structures in the Protein Data Bank. United Kingdom: N. p., 2017. Web. https://doi.org/10.1016/j.str.2017.10.009.
Gore, Swanand, Sanz García, Eduardo, Hendrickx, Pieter M. S., Gutmanas, Aleksandras, Westbrook, John D., Yang, Huanwang, Feng, Zukang, Baskaran, Kumaran, Berrisford, John M., Hudson, Brian P., Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Mading, Steve, Mak, Lora, Mukhopadhyay, Abhik, Oldfield, Thomas J., Patwardhan, Ardan, Peisach, Ezra, Sahni, Gaurav, Sekharan, Monica R., Sen, Sanchayita, Shao, Chenghua, Smart, Oliver S., Ulrich, Eldon L., Yamashita, Reiko, Quesada, Martha, Young, Jasmine Y., Nakamura, Haruki, Markley, John L., Berman, Helen M., Burley, Stephen K., Velankar, Sameer, & Kleywegt, Gerard J.. Validation of Structures in the Protein Data Bank. United Kingdom. https://doi.org/10.1016/j.str.2017.10.009
Gore, Swanand, Sanz García, Eduardo, Hendrickx, Pieter M. S., Gutmanas, Aleksandras, Westbrook, John D., Yang, Huanwang, Feng, Zukang, Baskaran, Kumaran, Berrisford, John M., Hudson, Brian P., Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Mading, Steve, Mak, Lora, Mukhopadhyay, Abhik, Oldfield, Thomas J., Patwardhan, Ardan, Peisach, Ezra, Sahni, Gaurav, Sekharan, Monica R., Sen, Sanchayita, Shao, Chenghua, Smart, Oliver S., Ulrich, Eldon L., Yamashita, Reiko, Quesada, Martha, Young, Jasmine Y., Nakamura, Haruki, Markley, John L., Berman, Helen M., Burley, Stephen K., Velankar, Sameer, and Kleywegt, Gerard J.. Fri . "Validation of Structures in the Protein Data Bank". United Kingdom. https://doi.org/10.1016/j.str.2017.10.009.
@article{osti_1410138,
title = {Validation of Structures in the Protein Data Bank},
author = {Gore, Swanand and Sanz García, Eduardo and Hendrickx, Pieter M. S. and Gutmanas, Aleksandras and Westbrook, John D. and Yang, Huanwang and Feng, Zukang and Baskaran, Kumaran and Berrisford, John M. and Hudson, Brian P. and Ikegawa, Yasuyo and Kobayashi, Naohiro and Lawson, Catherine L. and Mading, Steve and Mak, Lora and Mukhopadhyay, Abhik and Oldfield, Thomas J. and Patwardhan, Ardan and Peisach, Ezra and Sahni, Gaurav and Sekharan, Monica R. and Sen, Sanchayita and Shao, Chenghua and Smart, Oliver S. and Ulrich, Eldon L. and Yamashita, Reiko and Quesada, Martha and Young, Jasmine Y. and Nakamura, Haruki and Markley, John L. and Berman, Helen M. and Burley, Stephen K. and Velankar, Sameer and Kleywegt, Gerard J.},
abstractNote = {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.},
doi = {10.1016/j.str.2017.10.009},
journal = {Structure},
number = 12,
volume = 25,
place = {United Kingdom},
year = {2017},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.str.2017.10.009

Citation Metrics:
Cited by: 19 works
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Figures / Tables:

Figure 1 Figure 1: Summary Quality Metrics in the wwPDB Validation Reports. Sliders (top) and residue plots (bottom). (A) relatively good structure; (B) relatively poor structure. The solid sliders report on how a given structure ranks relative to all structures in the PDB. The open sliders report on the comparison with structuresmore » derived in a similar fashion (X-ray crystallographic structures are compared with other X-ray structures solved at a similar resolution, while NMR and EM structures are ranked relative to other NMR and EM structures in the PDB, respectively). Residue sequence plots flag residues that have unusual geometry features (i.e., bond length, bond angle, Ramachandran, RNA suiteness, or other torsion-angle outliers). Residues are color coded as follows: green, no geometric outliers; yellow, 1 type of outliers; orange 2 types of outliers; red, 3 or more types of outliers; gray, atomic coordinates not available; cyan, atomic coordinates are ill-defined by the NMR ensemble. For X-ray crystal structures, a red dot above a residue indicates a poor fit to electron density (RSRZ > 2).« less

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Works referencing / citing this record:

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach
journal, December 2018


Introduction to crystallographic refinement of macromolecular atomic models
journal, July 2019


Worldwide Protein Data Bank validation information: usage and trends
journal, March 2018

  • Smart, Oliver S.; Horský, Vladimír; Gore, Swanand
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 3
  • DOI: 10.1107/s2059798318003303

Structural biology data archiving - where we are and what lies ahead
journal, May 2018

  • Kleywegt, Gerard J.; Velankar, Sameer; Patwardhan, Ardan
  • FEBS Letters, Vol. 592, Issue 12
  • DOI: 10.1002/1873-3468.13086

Big data science at AMED-BINDS
journal, February 2020


Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3
journal, August 2018

  • Scietti, Luigi; Chiapparino, Antonella; De Giorgi, Francesca
  • Nature Communications, Vol. 9, Issue 1
  • DOI: 10.1038/s41467-018-05631-5

Identification and molecular mechanism of antithrombotic peptides from oyster proteins released in simulated gastro-intestinal digestion
journal, January 2019

  • Chen, Hui; Cheng, Shuzhen; Fan, Fengjiao
  • Food & Function, Vol. 10, Issue 9
  • DOI: 10.1039/c9fo01433k

Evolving data standards for cryo-EM structures
journal, January 2020

  • Lawson, Catherine L.; Berman, Helen M.; Chiu, Wah
  • Structural Dynamics, Vol. 7, Issue 1
  • DOI: 10.1063/1.5138589

Refining the macromolecular model – achieving the best agreement with the data from X-ray diffraction experiment
journal, September 2018


NMDA receptor channel gating control by the pre-M1 helix
journal, March 2020

  • McDaniel, Miranda J.; Ogden, Kevin K.; Kell, Steven A.
  • Journal of General Physiology, Vol. 152, Issue 4
  • DOI: 10.1085/jgp.201912362

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
journal, January 2018


RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
journal, October 2018

  • Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1004

Protein Data Bank: the single global archive for 3D macromolecular structure data
journal, October 2018

  • Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky949

VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes
journal, May 2019

  • Olechnovič, Kliment; Venclovas, Česlovas
  • Nucleic Acids Research, Vol. 47, Issue W1
  • DOI: 10.1093/nar/gkz367

Validation of ligands in macromolecular structures determined by X-ray crystallography
journal, March 2018

  • Smart, Oliver S.; Horský, Vladimír; Gore, Swanand
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 3
  • DOI: 10.1107/s2059798318002541

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
journal, June 2018

  • Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 7
  • DOI: 10.1107/s2059798318005764

Real-space refinement in PHENIX for cryo-EM and crystallography
journal, May 2018

  • Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
  • DOI: 10.1107/s2059798318006551

A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform
journal, August 2019


Synthesis, Biological Evaluation and Docking Studies of Benzoxazoles Derived from Thymoquinone
journal, December 2018

  • Glamočlija, Una; Padhye, Subhash; Špirtović-Halilović, Selma
  • Molecules, Vol. 23, Issue 12
  • DOI: 10.3390/molecules23123297

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.