I’m very excited that we’re going to be working with startup company Silicon Therapeutics on open source software development relating to binding free energy calculations. Silicon seeks to apply molecular simulations and free energy calculations to actually help design drugs, and is making major efforts to helping advance open source software in this area. Previously, Silicon announced their first Open Science Fellowship to Patrick Grinaway in John Chodera’s lab at MSKCC, supporting work on open source software for relative free energy calculations. [More…]
We’ve been helping to run the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind challenges for some time now, but the initiative is still unfunded. I’m excited that our revised grant proposal for the future of SAMPL has just been submitted to the NIH! While I normally wouldn’t post grant proposals, SAMPL is really a community resource, fueled by the community, so here’s a link to our plan for SAMPL’s future. [More…]
We’re super excited about the Statistical Assessment of Modeling of Proteins and Ligand (SAMPL) series of blind challenges, and the potential these have for driving real advancements in modeling in our field. These challenges not only provide an opportunity for blind, prospective testing of our methods, but they also provide a crowdsourcing model to drive innovation. Such approaches have a well-documented history of spurring progress in specific areas, such as in the XPrize, the Netflix Prize, or, closer to our field, the DREAM challenges or CASP for protein structure prediction. [More…]
Plans are starting to shape up for the SAMPL6 blind prediction challenge, coming later this year! (Our overall SAMPL initiative is still unfunded and we need your input, but we are able to proceed with SAMPL6).
SAMPL6 will focus on host-guest binding on some familiar systems, as well as logD prediction with known (provided) pKa values for a series of small organic compounds. [More…]