Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank

Abstract

SummaryBiomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB Restraint Violation Report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.Graphical AbstractHighlightsPDB Structure Validation Report expanded to include Restraint AnalysisNMR Exchange Format (NEF) and NMR-STAR for distance restraint representationStandard distance and dihedral restraint formats for model vs. restraint assessmentStandardized restraint formats provide interoperability between modeling programs