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Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB

  1. Pieter M. S. Hendrickx,
  2. Aleksandras Gutmanas*,
  3. Gerard J. Kleywegt*

Article first published online: 15 JAN 2013

DOI: 10.1002/prot.24213

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 81, Issue 4, pages 583–591, April 2013

Additional Information

How to Cite

Hendrickx, P. M. S., Gutmanas, A. and Kleywegt, G. J. (2013), Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB. Proteins, 81: 583–591. doi: 10.1002/prot.24213

Author Information

  1. Protein Data Bank in Europe, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

*Protein Data Bank in Europe, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

Publication History

  1. Issue published online: 8 MAR 2013
  2. Article first published online: 15 JAN 2013
  3. Accepted manuscript online: 23 NOV 2012 06:27AM EST
  4. Manuscript Accepted: 29 OCT 2012
  5. Manuscript Revised: 4 OCT 2012
  6. Manuscript Received: 2 AUG 2012

Funded by

  • European Molecular Biology Laboratory (EMBL)
  • Wellcome Trust. Grant Number: 088944
  • Funding for open access charge: Wellcome Trust UK Biotechnology and Biological Sciences Research Council. Grant Numbers: BB/E007511/1, BB/J007471/1

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Keywords:

  • Protein Data Bank;
  • nuclear magnetic resonance;
  • chemical shifts;
  • distance constraints;
  • angular constraints;
  • residual dipolar couplings

Abstract

We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. © Proteins 2013. © 2012 Wiley Periodicals, Inc.

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