We just released a new version of our “perpetual review” paper on benchmark sets for binding free energy calculations. This version adds new discussion on possible future benchmark sets, as well as on the need for workflow science. This paper is a bit of an experiment in publishing — we’re treating it sort of like software development, so it’s versioned, and we’re delighted to have community input, feedback, etc. [More…]
We had a great last year with four graduate students joining the lab and four graduating! Welcome Hannah, Martin, Chris and Tran! Congratulations to Guilherme, Camilla, Caitlin and Nathan!
The Chodera Lab recently started a document on best practices for software development in computational chemistry; we’ve contributed a small amount to it. It looks to be already quite useful as a reference/introduction, and they are seeking input and contributions. Check it out and join in! https://github.com/choderalab/software-development [More…]
We’ve been working on planning future iterations of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges, and have given a lot of thought to how to design SAMPL challenges in order to systematically advance predictive modeling for pharmaceutical drug discovery and molecular design. In our view, we need a series of blind predictive challenges specifically tailored to focus on the major challenges impairing accuracy. [More…]
We’ve migrated our website to be hosted on Amazon Web Services (AWS) and use WordPress. Let us know what you think.
David L. Mobley has submitted a review paper on benchmark sets for binding free energy calculations titled Predicting binding free energies: Frontiers and benchmarks to bioRxiv and Annual Reviews in Biophysics. Check out the related Github repo for more info. [More…]