Matthew Crown

Hi! I’m a recently submitted PhD student at Northumbria University working in bioinformatics/computational biology.

At work, I’m interested in building tools and pipelines for structural and functional annotation of proteins, viruses and metadata (check out my publications and repositories).

Im currently looking for jobs in tech-bio or biotech companies, with a particular interest in protein engineering. I hope to work on projects that have a positive impact on society and the environment. If you think I could be a good fit for your team, please get in touch!

Outside of work, I enjoy running, bouldering, cooking and tinkering with tech, and I’m a big fan of coffee, football and Formula 1.

1. ProCogGraph: A graph-based mapping of cognate ligand domain interactions

   Matthew Crown, and Matthew Bashton

   Bioinform. Adv., Oct 2024

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   Abstract Motivation Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docking and protein design. Since the last available cognate-ligand domain database was released, the PDB has grown significantly and new tools are available for measuring similarity and determining contacts. Results We present ProCogGraph, a graph database of cognate-ligand domain mappings in PDB structures. Building upon the work of the predecessor database, PROCOGNATE, we use data-driven approaches to develop thresholds and interaction modes. We explore new aspects of domain-cognate ligand interactions, including the chemical similarity of bound cognate ligands and how domain combinations influence cognate ligand binding. Finally, we use the graph to add specificity to partial EC IDs, showing that ProCogGraph can complete partial annotations systematically through assigned cognate ligands. Availability and Implementation The ProCogGraph pipeline, database and flat files are available at https://github.com/bashton-lab/ProCogGraph and https://doi.org/10.5281/zenodo.13165851. Supplementary information Supplementary data are available at Bioinformatics Advances online.

2. SPEAR: Systematic ProtEin AnnotatoR

   Matthew Crown, Natália Teruel, Rafael Najmanovich, and 1 more author

   Bioinformatics, Aug 2022

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   SUMMARY: We present Systematic ProtEin AnnotatoR (SPEAR), a lightweight and rapid SARS-CoV-2 variant annotation and scoring tool, for identifying mutations contributing to potential immune escape and transmissibility (ACE2 binding) at point of sequencing. SPEAR can be used in the field to evaluate genomic surveillance results in real time and features a powerful interactive data visualization report. AVAILABILITY AND IMPLEMENTATION: SPEAR and documentation are freely available on GitHub: https://github.com/m-crown/SPEAR and are implemented in Python and installable via Conda environment. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.