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.
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
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).
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
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
- Three-month PIPS placement at benevolent.ai, a growing company that uses machine learning approaches to predict drug candidates. My project involved developing an in-house tool as part of the biomedical team for use by drug discoverers.
- Eight-week placement at the University of São Paulo (summer 2013) on virtual screening to re-purpose existing drugs.
- Eight-week placement at Imperial College London (summer 2011) on computational modelling of ionic liquids.
- Member of the open source BioJulia project - wrote the BioStructures.jl package that deals with parsing and manipulating macromolecular structures. Have also made contributions to the Biopython project, written the Molly.jl package for molecular simulation in Julia and written some pdb-benchmarks.
- Lead web developer for the Write on Point project that gives applicants to university the skills to write an effective personal statement.
- Supervision of two ten-week MSc projects and a ten-week BSc project at Imperial, involving project design and regular meetings with the students.
- Demonstration in undergraduate and graduate computational practicals at Imperial and UCL.
- Peer reviewed 20 scientific papers, 1 funding proposal and was on the review committee for JuliaCon 2018.
Email: jgreener at mrc-lmb.cam.ac.uk