ArticleJournal of biomolecular NMR2013
PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
Article in Journal of biomolecular NMR, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
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- The NMR Exchange Format (NEF): Specification and Applications.bioRxiv : the preprint server for biology · 2026Article
- Protocol for deriving distance restraints from AlphaFold for use in solution NMR structure determination.STAR protocols · 2025Article
- Zinc-Induced Folding and Solution Structure of the Eponymous Novel Zinc Finger from the ZC4H2 Protein.Biomolecules · 2025Article
- NMR Spectroscopy for the Validation of AlphaFold2 Structures.bioRxiv : the preprint server for biology · 2025Article
- AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data.bioRxiv : the preprint server for biology · 2024Article
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- Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.Structure (London, England : 1993) · 2024Article
- Representing structures of the multiple conformational states of proteins.Current opinion in structural biology · 2023Review
- Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2023Article
- Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data.bioRxiv : the preprint server for biology · 2023Article
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- Structural and mutational analysis of MazE6-operator DNA complex provide insights into autoregulation of toxin-antitoxin systems.Communications biology · 2022Article
- Theta-Defensins to Counter COVID-19 as Furin Inhibitors:Computational and mathematical methods in medicine · 2022Article
- AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.Frontiers in molecular biosciences · 2022Article
- Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2.Proteins · 2021Article
- Article
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5 authors.
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Abstract
The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.
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