NEWS
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)
CADD GRC 2023 talk
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I’m thrilled to have the opportunity to speak about the COVID Moonshot (and its successor, ASAP) at the 2023 Computer Aided Drug Discovery Gordon Research Conference. A copy of my slides can be found here: [PDF]
Celebrating ten years at MSKCC
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Today, I had the privilege of giving the SKI Talk at MSKCC, and talk about what our lab has been up to the last few years. It’s been an amazing decade, and it was a pleasure to share some of the highlights since the last SKI Talk just four years ago.
You can find a copy of my talk slides here: [PDF]
RECOMB 2022 talk: The COVID Moonshot and the new ASAP AViDD Center
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I was delighted to have the opportunity to speak about the COVID Moonshot and our new ASAP AViDD Center. You can find a copy of my slides here: [PDF]
ICLR Machine Learning for Drug Discovery (MLDD) Workshop talk slides
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I am thrilled to have the opportunity to speak at the ICLR MLDD workshop. You can find a copy of my slides 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]
OpenEye CUP XXI talk - A Moonshot on Theory and Practice
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I was thrilled to be able to join the OpenEye CUP XXI meeting—the first meeting I have attended in person in two years (after the last OpenEye CUP meeting)—to present lessons learned from the COVID Moonshot. You can find a 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]
University of Toronto talk slides
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I was delighted to be able to visit Alán Aspuru-Guzik at the University of Toronto, and give a talk about our work on new tools for drug discovery and the COVID Moonshot. Slides can be downloaded here.
ACS Spring 2021 National Meeting: A Call to Action: The Many Roles of Computational Chemistry in Addressing COVID-19
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I had the honor of speaking about the COVID Moonshot in a session devoted to COVID-19 organized by JC Gumbart and Rommie Amaro, A Call to Action: The Many Roles of Computational Chemistry in Addressing COVID-19, earlier today. The slides are available here: [PDF]
Oxford Centre for Medicines Discovery talk
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I was delighted to have the opportunity to speak at the Oxford Centre for Medicines Discovery today! Here are my talk slides: [PDF]
Update on the COVID Moonshot for COVID/SARS CoV2 Rapid Research Reports #5
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You can find slides from John Chodera’s recent talk at the COVID/SARS CoV2 Rapid Research Reports #5 virtual meeting 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!
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.
Slides from the 2019 CADD GRC meeting in Mount Snow, VT
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I was thrilled to have a chance to speak in the free energy session at the 2019 Computer Aided Drug Design (CADD) Gordon Research Conference (GRC) in Mount Snow, VT on 15 July 2019! You can find a PDF copy of my slides here: [PDF]
PDF of my pitch for the 202X GRC concept: [PDF]
Slides from John Chodera's keynote talk at the NYC MACC/NYAGIM Symposium
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John Chodera gave the keynote talk (“Redesigning Drug Design (Together)”) at the Mid Atlantic Computational Chemistry (MACC) / New York Area Group for Informatics and Modeling (NYAGIM) joint Symposium at WCMC on 26 Apr 2019! You can find the slides from that talk here: [DOI]
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.
