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

Baskaran, K.; Ploskon, E.; Tejero, R.; Yokochi, M.; Harrus, D.; Liang, Y.; Peisach, E.; Persikova, I.; Ramelot, T. A.; Sekharan, M.; Tolchard, J.; Westbrook, J. D.; Bardiaux, B.; Schwieters, C.; Patwardhan, A.; Velankar, S.; Burley, S. K.; Kurisu, G.; Hoch, J. C.; Montelione, G. T.; Vuister, G. W.; Young, J. Y.

doi:10.1101/2024.01.15.575520

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bioRxiv · 10.1101/2024.01.15.575520

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

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Abstract

Biomolecular 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 Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/575520v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@bac5eforg.highwire.dtl.DTLVardef@190cdborg.highwire.dtl.DTLVardef@9b3d83org.highwire.dtl.DTLVardef@1e38ccc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPDB Structure Validation Report expanded to include Restraint Analysis C_LIO_LINMR Exchange Format (NEF) and NMR-STAR for distance restraint representation C_LIO_LIStandard distance and dihedral restraint formats for model vs. restraint assessment C_LIO_LIStandardized restraint formats provide interoperability between modeling programs C_LI

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Baskaran, K., Ploskon, E., Tejero, R., Yokochi, M., Harrus, D., Liang, Y., Peisach, E., Persikova, I., Ramelot, T. A., Sekharan, M., Tolchard, J., Westbrook, J. D., Bardiaux, B., Schwieters, C., Patwardhan, A., Velankar, S., Burley, S. K., Kurisu, G., Hoch, J. C., Montelione, G. T., Vuister, G. W., Young, J. Y.. 2024-01-17. Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank. https://doi.org/10.1101/2024.01.15.575520

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