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…]
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…]
Stefania Evoli, David L. Mobley, Rita Guzzi and Bruno Rizzuti
Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. [More…]
Scientific publishing faces challenges and changes induced by the same forces which have reshaped the news industry and are reshaping the traditional publishing industry. You could say that the Internet changes every information-centric industry, but some industries are slower to change than others.
Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. MobleyIn the recent SAMPL5 challenge, participants submitted predictions for cyclohexane/water distribution coefficients for a set of 53 small molecules. Distribution coefficients (log D) replace the hydration free energies that were a central part of the past five SAMPL challenges. A wide variety of computational methods were represented by the 76 submissionsfrom 18 participating groups.