Pre-deposition data validation services

• wwPDB validation service Stand-alone wwPDB validation service to generate wwPDB validation report.
• Coordinates versus Assigned Chemical Shifts Checker A tool to check Assigned Chemical Shift nomenclature versus Coordinate file nomenclature. This tool runs the same checks as will be run later when you deposit atomic coordinates with ADIT-NMR.
• MolProbity PDB Validation
• Protein Structure Validation suite (PSVS) is a useful tool for the assesment of protein structures generated by NMR and X-ray methods. PSVS is broadly applicable for structure quality assessment in structure biology projects.
• iCing Validation Package is part of the Common Interface for NMR structure Generation (CING) package.
• BMRB data visualization service will generate DEVise visualizations for uploaded NMR-STAR 3.1 data tables.
• LACS report generator is an automated tool for assignment outlier detection and correction of errors in referencing.
• CheckShift Chemical Shift Reference Check at Center of Applied Molecular Engineering, the University of Salzburg, Austria. It works on NMR-STAR 2.1, SHIFTX or TALOS files.

Downloadable data validation software

• LACS 64-bit linux binary (requires Matlab runtime), Matlab source code, and python wrappers
• Watto is a software package consisting of programs for analyzing, annotating, parsing, archiving, and disseminating experimental NMR data deposited by authors world wide into the PDB.

Format conversion tools

• Converts data files in various formats to NMR-STAR 3.1 for upload to ADIT-NMR. Input formats include NMRView, PIPP, Sparky, XEASY, as well as tab- and comma-delimited.
• Generate data table produces NMR-STAR 3.1 formatted tables for NMR data. (Use these as examples of NMR-STAR data files.)
• Assign ambiguity code simplifies assignment of chemical shift ambiguity codes.
• NMR resources and services from PDBe: a set of Python scripts that can read NMR data files and output them into a number of different formats.
• Convert NMR-STAR 3.1 table converts NMR-STAR 3.1 chemical shift tables to Sparky, NMRPipe/TALOS, XEASY, or NMR-STAR 2.1.

Conversion tools donated by the NMR community

• tab2bmrb convert chemical shift tables between publication format and NMR-STAR 2.1 format. Also included are tools to calculate random coil chemical shifts and NMR experimental pulse lengths for experiments dependent on 3JHN(CA)HA coupling constants.
• felix2bmrb software for converting FELIX chemical shift files to NMR-STAR 2.1 format.
• pipp2nmrstar software for converting PIPP chemical shift files to NMR-STAR 2.1 format.
• bmrb2talos script for converting chemical shift tables in BMRB entries to TALOS+ input files.
• cyana2xplor script for converting CYANA formatted files to XPLOR/CNS/PDB files.

• nightshift program for plotting simulated 2D and 3D NMR spectra from assigned chemical shifts of BMRB archive.
• Chenomx NMR Suite software suite to identify and quantify metabolites in NMR spectra.

Tools for NMR spectral analysis

• NMR Tool Box includes MagRO-NMRView, SPARTA validation tool and FitRobot
• SAS_CNS NMR assignment tool for solid-state NMR
• Olivia Objective, chemical shift library based, stereo-view assignment software
• xyza2pipe A cross conversion environment of multi dimensional NMR spectra

Tools for enhancing interoperability of BMRB

• BMRBxTool XML converter for NMR-STAR data
• BMRBoTool Ontology tool for NMR-STAR data
• BMSxNmrML nmrML converter for BMRB metabolomics entries
• BMRB Relational DB Snapshot Periodically updated BMRB Relational DB
• xsd2pgschema XML Schema based database replication tool
• owl-indexer Full-text index generator of OWL literal
• pdbx-validation A generation tool of alternative wwPDB validation information