Introducing the Chodera lab at the Memorial Sloan-Kettering Cancer Center

The Chodera laboratory at the Memorial Sloan-Kettering Cancer Center (MSKCC) has just received our new Folding@Home server hardware, allowing us to tap into the 10+ PFLOP/s of computing resources generously provided by the F@H Donor Community.  We’re excited to join this vibrant community and bring some F@H resources to bear on various problems in cancer we’re currently working on.

Our mission

Our mission is to completely redesign the way that therapeutics—especially anticancer drugs—are designed using computers, graphics processors (GPUs), distributed computing, robots, and whatever technology we can get our hands on.  We are striving to make the design of new cancer drugs much more of an engineering science, where state-of-the-art computer models quantitatively and accurately predict many aspects of drug behavior before they are synthesized.  We certainly won’t get there overnight—lots of hard work is needed to improve our algorithms, forcefields, and theory.   But by tapping into the enormous computing resources of F@H, we can more rapidly make predictions and then test them in our laboratory (with robots!) to quickly make improvements through learning from each cycle of prediction and validation.

Our server hardware

We are installing some heavy-duty servers to serve up F@H work units mainly to GPU users.  Our main server is a Dell R820 with 4x Intel Xeon E5-4620 2.2GHz processors and 256GB of RAM, which will also allow us to analyze incoming data “on the fly” to adaptively and intelligently make use of F@H Donor computing resources.  Our backup server is a Dell R620 with 2x Intel Xeon E5-2690 2.9GHz processors, also with 256GB of RAM.  These servers are both connected via SAS to a Dell MD3260 disk array containing 60x 4TB disks, providing 240TB of raw storage, or 192TB of usable storage with RAID6 to guard against data loss.

Expect more updates from us soon as we roll out our first big F@H projects.  We’ll tell you more about the science, the challenges, the technology, and our hope to transform the way cancer is treated and drugs are designed to treat important diseases.  For now, we’ve been busy moving into our new laboratory space and run our first robotic experiments!

Four-panel display of Chodera lab members performing a biophysical experiment.
Members of the Chodera lab conduct their first wetlab experiment in the Chodera lab at the Memorial Sloan-Kettering Cancer Center: isothermal titration calorimetry measurements of protein-ligand binding affinities.