Biology subjects

Brooksbank, E. J.

Publications and source records attributed to Brooksbank, E. J..

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↗

bioRxiv2026

The NMR Exchange Format (NEF): Specification and Applications

The NMR Exchange Format (NEF) is a community-driven standard for representing NMR experimental data in a consistent, interoperable, and machine-readable form. Built on the STAR syntax, NEF provides a structured framework for storing and exchanging chemical shifts, peak lists, various types of structural restraints, and related metadata, thus allowing for data exchange across software platforms. By enabling direct, lossless transfer of information, NEF simplifies multi-software workflows, improves reproducibility, and supports FAIR (Findable, Accessible, Interoperable, Reusable) data principles. We describe the NEF specification, its current implementation across commonly used NMR software packages, and its application in areas including biomolecular structure determination, metabolomics, and ligand screening. Testing demonstrates that NEF can be used to exchange complete datasets between programs without loss of information or functionality. We also outline recent developments and future directions, such as inclusion of NMR relaxation data and support for non-standard residue topologies. NEFs growing adoption highlights its potential as a unifying standard for NMR data, enabling more efficient, transparent and collaborative research.

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↗