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Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank

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posted on 2024-05-13, 15:01 authored by Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A Ramelot, Monica Sekharan, James Tolchard, John D Westbrook, Benjamin Bardiaux, Charles D Schwieters, Ardan Patwardhan, Sameer Velankar, Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, Gaetano T Montelione, Geerten VuisterGeerten Vuister, Jasmine Y Young

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 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.

History

Author affiliation

College of Life Sciences/Molecular & Cell Biology

Version

  • VoR (Version of Record)

Published in

Structure

Pagination

S0969-2126(24)00050-9

Publisher

Elsevier BV

issn

0969-2126

eissn

1878-4186

Copyright date

2024

Available date

2024-05-13

Spatial coverage

United States

Language

en

Deposited by

Professor Geerten Vuister

Deposit date

2024-05-09

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