2024 NCATS Assay Guidance Manual in silico drug discovery workshop

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I was honored to speak at the NCATS Assay Guidance Manual in silico drug discovery workshop, hosted virtually 23-24 Oct 2024. I presented an overview of modern physics-based free energy calculations for drug discovery, highlighting the open source ecosystem from Open Free Energy, Open Force Field, and other Open Molecular Software Foundation (OMSF) projects.

My slides are available via Google Slides (CC-BY 4.0)

OpenEye CUP XXIII talk: ML/MM REPEX/ATM FEP/MBAR RBFEs and You

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I had the privilege of being called on to give the final talk of this year’s OpenEye CUP XXIII to close an engaging meeting full of excitement for structure-based drug discovery. In this talk, I highlight the rapid work going on in machine learned (ML) potentials and their growing role in alchemical free energy calculations for structure-enabled drug discovery, and close with a provocative opportunity for the future of computer-aided drug discovery. [PDF]

Kate Holloway award symposium talk

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I’m thrilled to have the opportunity to speak at the ACS Award for Computers in Chemical & Pharmaceutical Research in honor of Kate Holloway, whose incredible career in drug discovery to date involves contributions to the invention of over sixty ligands for different therapeutic targets, including successful HIV inhibitors that have significantly changed patient outcomes for those living with AIDS. Kate’s tireless work to improve the field and visionary view on what computational chemistry is capable of are an inspiration to us all.

You can find a PDF copy of my slides here: [PDF]

NIH BISTI talk: Open science antiviral discovery with 
the covid moonshot 🌙 🚀
and the open source drug discovery ecosystem

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I had the great pleasure of speaking to the NIH Biomedical Information Science and Technology Initiative (BISTI) community on 3 Feb 2022 about open science antiviral drug discovery with the COVID Moonshot and how the open source computer-aided drug discovery ecosystem functions as a fantastic mechanism to enable collaboration to address major challenges in drug discovery. Open source software communities such as the Open Molecular Software Foundation (OMSF), which sponsors the Open Force Field Initiative and the Open Free Energy Consortium, and OpenMM, play a major role in this. Community-wide blind challenges, such as D3R, SAMPL, and the new CACHE effort (a CASP for computational hit-finding), are also collaborative open science engines that drive progress.

A PDF version of the slides I presented can be found here: [PDF]

Folding@home 20th Anniversary Livestream!

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Folding@home is twenty years old this year! It’s been a wild ride: Probing the fundamental nature of protein folding, organically growing the world’s first exaflops computing resource, and tackling COVID-19 drug discovery with free energy calculations at unprecedented scale. The project has produced hundreds of peer-reviewed scientific papers and enormous public datasets for researchers to mine.

We were lucky to celebrate some highlights from the past twenty years with Folding@home founder Vijay Pande, Greg Bowman (the current Director of the Folding@home Consortium), Sukrit Singh, ReadyPlayerEmma, and COVID Moonshot guests Alpha Lee and Frank von Delft who joined me to talk about the amazing progress the Moonshot has made over the past few months.

If you missed the livestream, you can watch the recorded stream here on twitch.

Slides from Labsgiving group meeting on software development best practices

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It’s become a tradition in the lab to have a Labsgiving group meeting the week of Thanksgiving! This year, I was on the group meeting rotation, and we were lucky enough to have our wonderful collaborators from the Andrea Volkamer lab at the Charité in Berlin join as well!

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I covered some topics on why we practice open science and open source software, and our current best practices for doing so. Best practices are ever evolving, and we are always learning ways to better practice our craft and share our work with the world. In that spirit, we have tried to capture much of our current practices in a GitHub repo to make it easier to gather feedback and continually refine our practices: [software development best practices]

I put together a short talk covering some of the highlights of our best practices. In case it’s useful, you can find the PDF slides here: [PDF]

Happy Thanksgiving, all!

~ John

Slides from John Chodera's talk at GCC 2019

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I was thrilled to have had the opportunity to speak at the 15th German Conference on Cheminformatics (GCC 2019) in Mainz! You can find a PDF version of my slides here: [PDF] [reduced size PDF]

I’m also tremendously excited that GCC 2020 will take place 1-5 Nov 2020 and will feature two days of EuroSAMPL, our first international SAMPL challenges meeting! Stay tuned for more information.