Wattos

Wattos parses and analyzes experimental NMR spectroscopy data to prepare, validate, and standardize distance and dihedral restraints and coordinates for structural biology applications.

Key Features:

• Data parsing and preparation: Parses NMR-derived distance and dihedral angle restraints and prepares them consistently for downstream analysis.
• Integration with CcpNmr FormatConverter: Integrates with CcpNmr FormatConverter to semi-automate restraint preparation workflows.
• Advanced analysis modules (Aqua): Implements modules such as Aqua within the BMRB framework to scrutinize sets of distance restraints for inconsistencies, redundancies, NOE completeness, classification, and violations relative to original coordinates.
• Flagging and hydrogen recalculation: Identifies restraints that cannot be associated with known nomenclature and recalculates hydrogen atom coordinates from heavy atom positions.
• Repository integration: Parses, annotates, and prepares experimental NMR data deposited in the Protein Data Bank (PDB) and BioMagResBank (BMRB) for archiving and dissemination.
• IUPAC consistency enforcement: Ensures consistency between restraint and coordinate data by aligning nomenclature with IUPAC conventions.
• Export and conversion formats: Produces data in NMR-STAR and CCPN XML and in formats compatible with CNS and CYANA.

Scientific Applications:

• Database Of Converted Restraints (DOCR): Standardizes restraint and coordinate data and aligns them with IUPAC conventions for downstream structural analyses.
• Filtered Restraints Database (FRED): A curated subset derived from DOCR intended for test calculation protocols, longitudinal analyses, and validation of NMR-derived restraints.

Methodology:

Applies stringent inclusion criteria focused on unique, monomeric proteins with available experimental NMR data and PDB coordinates, and parses and consistently prepares restraint and coordinate files.