Celebrating six years of the Chodera lab!

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]

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!


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.

ICMS Edinburgh Workshop on multiscale methods for stochastic dynamical systems in biology


The International Centre for Mathematical Sciences (ICMS) held a fantastic workshop over the last week here in Edinburgh, covering multiscale methods for stochastic dynamical systems in biology.  It's phenomenal that there are organizations that are strongly committed to supporting the exciting interface between mathematics and the biological sciences, and the enthusiastic discussions at this meeting were a reflection of the enormous potential that work at this interface holds for both fields. These workshops also attempt to engage the public to communicate the importance of this interdisciplinary work through a public lecture series, with Sarah A. Harris delivering a talk on the interface of physics and biology.

PDF slides from my talk are available online, and the talks were all recorded to be posted online shortly.

OpenEye JCUP VI talk slides

I'm thrilled to have the opportunity to speak to a distinguished collection of scientists from pharma and academia here in Tokyo at the OpenEye JCUP VI drug discovery meeting.

I thought it might help to post a PDF copy of my slides where I discuss how experiments and theory can work together to gain insight into how to improve quantitative predictive models for drug discovery.

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.

Talk slides for New York Structural Biology Discussion Group (NYSBDG) posted

I had a fantastic time hearing about all of the exciting science going on in NY at the New York Structural Biology Discussion Group 10th Winter Meeting hosted at the New York Academy of Sciences last week.  I had several requests to make my talk slides available, so I'm posting them here in PDF form:

John Chodera's talk slides from the NYSBDG meeting on Wed 21 Jan

Looking forward to many great future meetings of the NYSBDG!

Kyle Beauchamp's PyData NYC 2014 talk: Engineering a full Python stack for biophysical computation

Postdoc Kyle Beaucamp gave a talk about our omnia.md Python stack for biophysical computation at PyData NYC 2014.  The whole talk is now available online:

Youtube link:

Slides for the talk can be found here:

Engineering new therapeutics is hard--and getting harder. Accurate physical modeling promises to improve the way we design drugs, but the necessary open source infrastructure is lacking. The Omnia Consortium---a collaboration of multiple academic laboratories working on physical modeling tools for drug discovery---is producing a suite of open-source tools for understanding drugs, proteins, and the biomolecular mechanisms of disease. Our Python-centric software stack is uses Python, Cython, C++, and CUDA/OpenCL to achieve bleeding-edge performance. Part of our stack (OpenMM) is also implemented on the Folding@Home distributed computing project and currently runs on tens of thousands of high-end GPUs around the world, producing over 18PFLOP/s of computational power. In our talk, we will introduce biophysical simulation and its application to understanding mechanisms of disease and its potential for designing new therapeutics. We will discuss the challenges in building robust tools for automating and scaling up biophysical simulations, compared with the relatively mature tools already available for modern data science. We will describe some of the tools in our stack (OpenMM, MDTraj, MSMBuilder, Yank) and how we use the conda packaging environment to facilitate distribution of our domain-specific code. Finally, we will discuss our plans to improve physical models and study drug resistance using iterative cycles of modeling and automated biophysical experiments performed at Memorial Sloan-Kettering Cancer Center.