Vivaldi

A web-based service for the analysis, visualization and validation of nuclear magnetic resonance (NMR) structures in the Protein Data Bank. 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. A user-friendly interface, including a 3D viewer, tightly coupled with charts and tables, enables both experts and non-experts in NMR structure determination to analyze NMR ensembles and to assess their quality. 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 specifications

Web

Information

Unique identifier	OMICS_13260
Name	Vivaldi
Alternative name	VIsualization and VALidation Display
Interface	Web user interface
Restrictions to use	None
Input data	A protein ID
Output data	Charts and graphs
Programming languages	Javascript
Computer skills	Basic
Stability	Stable
Maintained	Yes

Maintainer

Aleksandras Gutmanas

Publication for VIsualization and VALidation Display

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

2013 Proteins

PMCID: 3618379

PMID: 23180575

DOI: 10.1002/prot.24213

Vivaldi institution(s)

Protein Data Bank in Europe, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Vivaldi funding source(s)

European Molecular Biology Laboratory (EMBL); Wellcome Trust (grant No. 088944); UK Biotechnology and Biological Sciences Research Council (grants No. BB/E007511/1, No. BB/J007471/1)

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