Joe Greener

I am a group leader at the MRC Laboratory of Molecular Biology working on improving molecular simulations. My group page is here and my entry on the LMB website is here. I am currently looking to grow the group. You can also find me on Twitter and GitHub.

My interests include molecular simulation, protein structures, software development and open science. Currently my work aims to use the concept of differentiable programming to improve the force fields used to simulate biomolecules, enabling us to better study disordered proteins and protein-ligand interactions.

Previously I was a research fellow (postdoc) in the Bioinformatics Group at University College London (UCL) and a PhD student in the Structural Bioinformatics Group at Imperial College London.

Modulation of adenylate cyclase

Publications

Google Scholar page

Yu CWH, Fischer ES, Greener JG, Yang J, Zhang Z, Freund SMV, Barford D. Molecular mechanism of Mad2 conformational conversion promoted by the Mad2-interaction motif of Cdc20, bioRxiv (2024) - link

Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, Chemical Science 15, 4897-4909 (2024) - link - code

Roesch E, Greener JG, MacLean AL, Nassar H, Rackauckas C, Holy TE and Stumpf MPH. Julia for biologists, Nature Methods 20, 655-664 (2023) - link

Greener JG and Jamali K. Fast protein structure searching using structure graph embeddings, bioRxiv (2022) - link - code

Greener JG*, Kandathil SM*, Moffat L and Jones DT. A guide to machine learning for biologists, Nature Reviews Molecular Cell Biology 23, 40-55 (2022) - link - open link

Kandathil SM, Greener JG, Lau AM and Jones DT. Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterized proteins, Proceedings of the National Academy of Sciences 119(4), e2113348119 (2022) - link - code

Moffat L, Greener JG and Jones DT. Using AlphaFold for Rapid and Accurate Fixed Backbone Protein Design, bioRxiv (2021) - link

Greener JG and Jones DT. Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins, PLoS ONE 16(9), e0256990 (2021) - link - code

Greener JG*, Desai N*, Kandathil SM and Jones DT. Near-complete protein structural modelling of the minimal genome, arXiv 2007.06623 (2020) - link

Greener JG, Selvaraj J and Ward BJ. BioStructures.jl: read, write and manipulate macromolecular structures in Julia, Bioinformatics 36(14), 4206-4207 (2020) - link - open link - code

Greener JG*, Kandathil SM* and Jones DT. Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints, Nature Communications 10:3977 (2019) - link - website - code

Kandathil SM, Greener JG and Jones DT. Recent Developments in Deep Learning Applied to Protein Structure Prediction, Proteins 87(12), 1179-1189 (2019) - link

Kandathil SM, Greener JG and Jones DT. Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13, Proteins 87(12), 1092-1099 (2019) - link - code

Greener JG*, Moffat L* and Jones DT. Design of metalloproteins and novel protein folds using variational autoencoders, Scientific Reports 8:16189 (2018) - link - code

Craven GB, Affron DP, Allen CE, Matthies S, Greener JG, Morgan RML, Tate EW, Armstrong A and Mann DJ. High-Throughput Kinetic Analysis for Target-Directed Covalent Ligand Discovery, Angewandte Chemie International Edition 57(19), 5257-5261 (2018) - link

Greener JG and Sternberg MJE. Structure-based prediction of protein allostery, Current Opinion in Structural Biology 50, 1-8 (2018) - link

Greener JG, Filippis I and Sternberg MJE. Predicting protein dynamics and allostery using multi-protein atomic distance constraints, Structure 25, 546-558 (2017) - link - code

Greener JG and Sternberg MJE. AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis, BMC Bioinformatics 16:335 (2015) - link - website - code

Software

Some software I have written or contributed to:

There is more software associated with a few of the papers listed above.

Talks

Enzyme Conference 2024 (Mar 2024) - video - slides

Talks and practical at SINEQ summer school, École des ponts ParisTech (Sep 2023) - slides - notebook

Talk at Institute of Genetics and Cancer, University of Edinburgh (Mar 2023) - slides

Enzyme Conference 2023 (Feb 2023) - video - slides

Crick Christmas Lecture 2022 (Dec 2022) - slides

JuliaMolSim minisymposium at JuliaCon 2022 (Jul 2022) - video - slides

8th Annual CCP-BioSim Conference invited talk (Jun 2022) - slides

Lennard Jones Centre (May 2022) - video - slides

Scientific Machine Learning Webinar Series (Mar 2022) - video - slides

Microsoft Research New England ML Ideas Lunch (Mar 2021) - slides

Imperial College Computational Biology Society (Nov 2020) - slides

KQ Codes Technical Social (Jan 2020) - slides.

3DSIG meeting at ISMB (Jul 2019) - video - slides.

London Julia Meetup group (Jun 2019) - slides.

Friday Wrap talk at Institute of Structural and Molecular Biology (May 2019) - slides.

3DSIG meeting at ISMB (Jul 2016).

Bioinformatics London Meetup group (Apr 2016).

Awards

Warren DeLano Structural Bioinformatics and Computational Biophysics Award for best presentation at 3DSIG 2016.

Awarded ISMB/ECCB Travel Fellowship to attend ISMB 2019 by 3DSIG and ISCB.

Prize for highest mark in MSc class (2014).

Runner-up prize for best presentation at Imperial College London Department of Life Sciences Research Day (2017).

CC BY 4.0 Joe Greener. Last modified: March 27, 2024. Website built with Franklin.jl and the Julia programming language.