Joe Greener

MRC Laboratory of Molecular Biology

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I am an independent researcher at the MRC Laboratory of Molecular Biology working on improving molecular simulations. 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.

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 proteins, enabling us to better study disordered proteins and protein aggregation - see more on my LMB web page. You can also find me on Twitter.

Modulation of adenylate cyclase

Publications

Google Scholar page

Greener JG*, Kandathil SM*, Moffat L and Jones DT. A guide to machine learning for biologists, Nature Reviews Molecular Cell Biology (2021) - link - open link

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 (2021) 16(9), e0256990 - link - code

Kandathil SM, Greener JG, Lau AM and Jones DT. Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterised proteins, bioRxiv (2020) - link - code

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

Greener JG, Selvaraj J and Ward BJ. BioStructures.jl: read, write and manipulate macromolecular structures in Julia, Bioinformatics (2020) 36(14), 4206-4207 - 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 (2019) 10:3977 - link - website - code

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

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

Greener JG*, Moffat L* and Jones DT. Design of metalloproteins and novel protein folds using variational autoencoders, Scientific Reports (2018) 8:16189 - 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 (2018) 57(19), 5257-5261 - link

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

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

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

Talks

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).

Education

2014-2017 - Imperial College London - PhD in Structural Bioinformatics - Funded by BBSRC

2013-2014 - Imperial College London - MSc Bioinformatics and Theoretical Systems Biology - Funded by BBSRC - Distinction

2009-2013 - Emmanuel College, University of Cambridge - MSci and BA Hons Natural Sciences (Chemistry) - 2.1 classification in all years

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).

Experience and skills

Contact

Email: jgreener at mrc-lmb.cam.ac.uk

Twitter: @jgreener64