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PMID: 23180575 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.

Proteins ·Vol. 81 ·No. 4 ·2013-04-00 ·Pages 583-91

Hendrickx PM, Gutmanas A, Kleywegt GJ

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.

MeSH Terms
Bacterial Proteins/chemistry Databases, Protein Helicobacter pylori/chemistry Internet Models, Molecular Nuclear Magnetic Resonance, Biomolecular Protein Conformation Pseudomonas aeruginosa/chemistry Software
Chemicals
Bacterial Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Hendrickx Pieter M S
Protein Data Bank in Europe, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Gutmanas Aleksandras
Kleywegt Gerard J
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Article Info
Journal
Proteins
Abbr.
Proteins
ISSN
1097-0134
DOI
10.1002/prot.24213
Published
2013-04-00
Epub
2013-00-15
Pages
583-91
Language
English
Region
United States
NLM ID
8700181
PMCID
PMC3618379
Subset
IM
Grants
Wellcome Trust · 088944 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/J007471/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/E007511/1 · United Kingdom
External Links
PubMed source DOI: 10.1002/prot.24213 PMC Full Text View journal details
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