Development and benchmarking of Open Force Field 2.0.0---the Sage small molecule force field

Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang L-P, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL
Journal of Chemical Theory and Computation 19:3251, 2023 [DOI] [chemRxiv] [GitHub] [examples]

We present a new generation of small molecule force field for molecular design from the Open Force Field Initiative fit to both quantum chemical and experimental liquid mixture data

Development and benchmarking of Open Force Field v1.0.0, the Parsley small molecule force field

Yudong Qiu, Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C Bannan, Trevor Gokey, Victoria T Lim, Chaya Stern, Andrea Rizzi, Xavier Lucas, Bryon Tjanaka, Michael R Shirts, Michael Gilson, John D. Chodera, Christopher I Bayly, David Mobley, Lee-Ping Wang
Preprint ahead of publication: [chemRxiv] [force fields] [Open Force Field Initiative]

We present a new, modern small molecule force field for molecular design from the Open Force Field Initiative, a large industry-academic collaboration that focuses on open science, open data, and modern open source infrastructure.

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, and John D. Chodera
Journal of Computer Aided Molecular Design 34:601, 2020. [DOI] [PDF] [bioRxiv] [GitHub]

To assess the relative efficiencies of alchemical binding free energy calculations, the SAMPL6 SAMPLing challenge asked participants to submit predictions as a function of computer effort for the same force field and charge model. Surprisingly, we found that most molecular simulation codes cannot agree on the binding free energy was, even for the same force field.

Overview of the SAMPL6 host-guest binding affinity prediction challenge

Andrea Rizzi, Steven Murkli, John N. McNeill, Wei Yao, Matthew Sullivan, Michael K. Gilson, Michael W. Chiu, Lyle Isaacs, Bruce C. Gibb, David L. Mobley*, John D. Chodera*
* denotes co-corresponding authors
Journal of Computer-Aided Molecular Design special issue on SAMPL6, 32:937, 2018. [DOI] [bioRxiv] [GitHub]

We present an overview of the host-guest systems and participant performance for the SAMPL6 host-guest blind affinity prediction challenges, assessing how well various physical modeling approaches were able to predict ligand binding affinities for simple ligand recognition problems where receptor sampling and protonation state effects are eliminated due to the simplicity of supramolecular hosts. We find that progress is now stagnated likely due to force field limitations.