Biology subjects

Vuister, G. W.

Publications and source records attributed to Vuister, G. W..

3 recordsLinked to original sources

bioRxiv2026

CcpNmr AnalysisDynamics: a unified framework for NMR dynamics data analysis

Nuclear Magnetic Resonance (NMR) relaxation experiments provide a powerful residue-resolved access to biomolecular dynamics across a wide range of timescales. Unfortunately, the quantitative analysis of the relaxation data remains distributed across specialised and often disconnected tools. Here, we present CcpNmr AnalysisDynamics, the latest addition to the CcpNmr Analysis program suite, providing an integrated framework for relaxation analysis, exchange-aware interpretation and dynamical modelling. The platform unifies relaxation-rate extraction, diagnostic validation, model-based analysis and structural visualisation within reproducible workflows, while supporting future extension through a robust application programming interface and plugin architecture. We introduce ModelAnalysis (ModA), a new analysis engine based on the Lipari-Szabo formalism that incorporates robust optimisation, uncertainty estimation and model-selection strategies designed for heterogeneous relaxation datasets. The framework also supports exchange-focused analysis and integration with specialised external modelling tools, allowing relaxation anomalies to be followed from initial detection to more detailed interpretation. The applicability and reliability of AnalysisDynamics are demonstrated through systematic re-analysis and validation of curated relaxation datasets from the Biological Magnetic Resonance Data Bank. These analyses enable assessment of data consistency, dynamic parameters and model reliability across magnetic fields, providing a reproducible route from NMR relaxation measurements to structure-linked interpretation of biomolecular dynamics.

biochemistry↗

bioRxiv2024

The CcpNmr Analysis Simulated Metabolomics Database (CASMDB): An Open-Source Collection of Metabolite Annotation Data for 1D 1H NMR-Based Metabolomics

Databases are invaluable for the identification of individual metabolites in untargeted metabolomics analyses, providing annotated pure metabolite references that allow for comparisons with experimentally collected mixture samples. Despite the value of an extensive reference database, publicly available databases for NMR-based metabolomics are often incomplete with respect to experimental conditions and derived NMR annotation parameters, such as peak positions. Hence, they are not designed for visualising the reference spectra alongside an experimental sample spectrum of interest, thus limiting the usefulness of the database. As a consequence, researchers have resorted to their own user- or application based database implementations. In this paper we describe the collection, remediation and integration of annotation data from the publicly available HMDB, BRMB and GISMO NMR metabolomics databases to build the CcpNmr Analysis Simulated Metabolomics Database (CASMDB) that contains 1932 unique metabolite entries. This database, in concert with the AnalysisMetabolomics programme, also allows or accurate simulation of spectra at arbitrary field strengths. Together, these tools underpin the visualising of experimental and simulated metabolite references and their usage in 1D 1H NMR-based metabolomics studies.

biochemistry↗

bioRxiv2024

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

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

bioinformatics↗