Barcelona MMSML talk: Teaching free energy calculations to learn

/

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

/

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]

NeurIPS 2020 talk

/
neurips-talk-graphic.jpg

John Chodera will be presenting at NeurIPS 2020 on learning biomolecular potential energy functions!

[video] [PDF]

The talk recording link will eventually be posted here, but in the meantime, you can find links to the preprints and code mentioned in the talk below:

gimlet: graph convolutional networks for partial charge assignment
preprint: https://arxiv.org/abs/1909.07903
code: http://github.com/choderalab/gimlet  

espaloma: end-to-end differentiable assignment of force field parameters
preprint: https://arxiv.org/abs/2010.01196 
code: https://github.com/choderalab/espaloma 


qmlify: hybrid QML/MM alchemical free energy calculations for protein-ligand binding
preprint: https://doi.org/10.1101/2020.07.29.227959
code: https://github.com/choderalab/qmlify


neutromeratio: alchemical free energy calculations with fully QML potentials for tautomer ratio prediction
preprint: https://doi.org/10.1101/2020.10.24.353318
code: https://github.com/choderalab/neutromeratio 

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

/
drugmsm.jpg
drugalchemy.jpg

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.

Fourth Alchemical Free Energy Calculations in Drug Design meeting at Vertex

/

The fourth Alchemical Free Energy Calculations in Drug Discovery workshop is already underway, held once again at the beautiful Vertex facility in Boston. We're livetweeting the meeting for those who can't make it, and have set up a new Slack team to keep the conversation going after the meeting. There's even a job postings page to keep track of the abundant new jobs in computational chemistry and alchemical free energy calculations in industry and academia this field has created. We're thrilled to see so much activity, how far the field is come, and certainly how far the field has left to go.

Slides from my talk can be found here in PDF format.

CECAM Workshop on developing interoperable and portable molecular simulation software libraries

/

I'm excited to be participating in the CECAM Workshop on Developing Interoperable and Portable Molecular Simulation  Software Libraries this week at the Forschungszentrum Jülich, organized by Julien Michel, along with Christopher Woods, Peter Eastman, and Gareth Tribello.

Slides and materials used during the workshop can be found here:

  • Examples and materials: https://github.com/choderalab/cecam-2015-julich-workshop

The Chodera lab is headed to the Biophysical Society Meeting in Baltimore

/

Four members of the Chodera lab will be headed to the Feb 7-11 Biophysical Society Meeting in Baltimore, MD!
Postdocs Sonya Hanson and Kyle Beauchamp will both be giving talks:

In addition, Sonya Hanson will serve as an official guest blogger for the BPS 2015 meeting!  Be sure to tune into the official BPS Blog to follow along!

Talk slides will be posted after the conference.

Rumor has it the lab will also make a brief appearance at the Society for Laboratory Automation and Screening SLAS2015 conference in Washington DC.