At Silicon Therapeutics, we use physics driven approaches to create lasting therapeutic and target franchises to impact human disease.

May 27, 2017

Silicon Therapeutics Announces Recipient of the First Open Science Fellowship

Boston – May 27, 2017: Silicon Therapeutics, an integrated computational drug discovery company creating novel small molecule therapeutics for diseases with challenging protein targets, is pleased to announce that the first Open Science Fellowship will be awarded to the laboratory of Dr. John D. Chodera at Memorial Sloan Kettering Cancer Center (MSK). The fellowship is designed to advance the open science movement within the drug discovery industry, facilitating access to scientific knowledge, methods, and data. Patrick Grinaway, a graduate student in the Chodera Lab, will lead the development efforts of the project, entitled “Development of efficient open source free energy-based lead optimization algorithms.” The work will build upon the open source GPU-accelerated OpenMM molecular simulation platform to develop advanced relative binding free energy methods, which can be used for predicting the binding affinity and selectivity of ligands to targets.

“Open science is an important part of our culture at Silicon Therapeutics. The Open Science Fellowship reflects our commitment to support the dissemination of research in areas such as molecular simulation techniques that have broad potential utility,” said Dr. Woody Sherman, CSO at Silicon Therapeutics. ”We are pleased to support a very talented graduate student and the Chodera Lab with this fellowship. The Chodera Lab has been a strong proponent of the open science movement and is an established leader in the field of molecular simulations, especially related to free energy calculations. Through a close collaboration facilitated by this fellowship, we will implement relative binding free energy calculations within the OpenMM platform to efficiently predict accurate protein-ligand binding affinities. In addition, we are very excited to implement a new method formulated in the Chodera Lab to simultaneously simulate many ligands within one calculation, thereby greatly expanding the chemical space that can be explored in drug discovery projects.”

This particular fellowship will build upon a class of physics-based simulation methods known as alchemical free energy calculations that allow for the prediction of binding affinities (and other physical properties) using alchemical perturbations that transform initial molecules into new molecules in silico. This project will leverage decades of academic research to bring relative binding free energy calculations into the Omnia consortium of tools built upon OpenMM [], a modern open source ecosystem for molecular modeling and simulation.

“Our laboratory is committed to exploring next-generation technologies for drug discovery by building high quality open source tools that permit rapid exploration and evaluation of promising new algorithms,” said Dr. Chodera. “We’re thrilled that Silicon Therapeutics is committed to support the development of high quality open source science for drug discovery.”


Silicon Therapeutics, the first fully integrated computational drug discovery company, is focused on developing novel medicines for diseases with targets that are currently considered to be challenging for traditional approaches. Our INSITE platform closely represents the real dynamic nature of targets using accurate all-atom simulations, enabling us to discover, design, and optimize compounds for targets that were previously considered “undruggable.” Our science, our team, and our mission are focused on applying advanced physics-based computational technologies to build and progress a pipeline of innovative medicines for patients. Silicon Therapeutics is headquartered in Boston, MA, USA with offices in Shanghai, China. Learn more at