Barcelona MMSML talk: Teaching free energy calculations to learn

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I was excited to attend the Barcelona MMSML workshop, which brought together a fantastic set of folks to discuss the future of machine learning in molecular simulation.

The slides to my talk, Teaching free energy calculations to learn, are available here: [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]

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.

Celebrating six years of the Chodera lab!

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The Chodera lab turns six years old on 1 Nov 2018! It’s been an exciting six years, having submitted or published thirty-five papers and having twenty-four trainees pass into or through the lab since then. To celebrate, John Chodera was asked to give a Sloan Kettering Institute (SKI) talk highlighting some of the exciting accomplishments and future directions. You can find the video of the whole talk here: [YouTube] [PDF Slides]

Check out more videos at the Chodera lab YouTube Channel.

2018 Workshop on Free Energy Methods, Kinetics and Markov State Models in Drug Design: Videos are up!

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The 2018 Workshop on Free Energy Methods, Kinetics and Markov State Models in Drug Design held at the Novartis NIBR campus in Cambridge, MA was a huge success! You can read some of the livetweeting by following #drugalchemy and #drugmsm on twitter, and catch up on talks you may have missed by going through our YouTube video playlist featuring recordings of all talks where the speakers consented to being recorded.

Special thanks to lead organizers Michael Schnieders and Greg Bowman, the fantastic panel of organizers, postdoc Levi Naden and Novartis Investigator Callum Dickson for wrangling A/V and venue details, Jose Duca for graciously allowing us to use the NIBR site, the Novartis A/V team, keynote speaker Mark Murcko, our hosts at Novartis, and all our wonderful speakers and participants for making this a success.