Literature DB >> 24010715

Recommendations of the wwPDB NMR Validation Task Force.

Gaetano T Montelione1, Michael Nilges, Ad Bax, Peter Güntert, Torsten Herrmann, Jane S Richardson, Charles D Schwieters, Wim F Vranken, Geerten W Vuister, David S Wishart, Helen M Berman, Gerard J Kleywegt, John L Markley.   

Abstract

As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 24010715      PMCID: PMC3884077          DOI: 10.1016/j.str.2013.07.021

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  53 in total

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Authors:  Jill Trewhella; Wayne A Hendrickson; Gerard J Kleywegt; Andrej Sali; Mamoru Sato; Torsten Schwede; Dmitri I Svergun; John A Tainer; John Westbrook; Helen M Berman
Journal:  Structure       Date:  2013-06-04       Impact factor: 5.006

5.  Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications.

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6.  Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation.

Authors:  A T Brünger; G M Clore; A M Gronenborn; R Saffrich; M Nilges
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Journal:  J Biomol NMR       Date:  2012-07-03       Impact factor: 2.835

8.  Objective identification of residue ranges for the superposition of protein structures.

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Authors:  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; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Helen M Berman; Wah Chiu; Gerard J Kleywegt; Catherine L Lawson
Journal:  Structure       Date:  2012-02-08       Impact factor: 5.006

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Journal:  PLoS Comput Biol       Date:  2008-02       Impact factor: 4.475

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  80 in total

Review 1.  A community resource of experimental data for NMR / X-ray crystal structure pairs.

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Journal:  Protein Sci       Date:  2015-09-22       Impact factor: 6.725

2.  OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Authors:  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; Luigi Di Costanzo; Dimitris Dimitropoulos; Guanghua Gao; Sutapa Ghosh; Swanand Gore; Vladimir Guranovic; Pieter M S Hendrickx; Brian P Hudson; Reiko Igarashi; Yasuyo Ikegawa; Naohiro Kobayashi; Catherine L Lawson; Yuhe Liang; Steve Mading; Lora Mak; M Saqib Mir; Abhik Mukhopadhyay; Ardan Patwardhan; Irina Persikova; Luana Rinaldi; Eduardo Sanz-Garcia; Monica R Sekharan; Chenghua Shao; G Jawahar Swaminathan; Lihua Tan; Eldon L Ulrich; Glen van Ginkel; Reiko Yamashita; Huanwang Yang; Marina A Zhuravleva; Martha Quesada; Gerard J Kleywegt; Helen M Berman; John L Markley; Haruki Nakamura; Sameer Velankar; Stephen K Burley
Journal:  Structure       Date:  2017-02-09       Impact factor: 5.006

3.  CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO.

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4.  The Protein Data Bank Archive.

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5.  A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions.

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Review 6.  Principles for Integrative Structural Biology Studies.

Authors:  Michael P Rout; Andrej Sali
Journal:  Cell       Date:  2019-05-30       Impact factor: 41.582

7.  How community has shaped the Protein Data Bank.

Authors:  Helen M Berman; Gerard J Kleywegt; Haruki Nakamura; John L Markley
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

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

Authors:  Chenghua Shao; Huanwang Yang; John D Westbrook; Jasmine Y Young; Christine Zardecki; Stephen K Burley
Journal:  Structure       Date:  2017-02-16       Impact factor: 5.006

9.  The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.

Authors:  David A Snyder; Jennifer Grullon; Yuanpeng J Huang; Roberto Tejero; Gaetano T Montelione
Journal:  Proteins       Date:  2014-02

10.  New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.

Authors:  Clare-Louise Towse; Steven J Rysavy; Ivan M Vulovic; Valerie Daggett
Journal:  Structure       Date:  2016-01-05       Impact factor: 5.006

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