CompChem Research Scientist – Sr., Principal

Role Overview

• Own the binding free energy function
• Take responsibility for small molecule binding free energy calculations that feed directly into project decision making
• Define best practice protocols across programs, and evolve them as the platform improves
• Optimize and improve existing methods, not just run them
• Start from existing methods and code bases (for example FEP, TI, and related alchemical / free energy workflows) and improve them for both speed and accuracy
• Identify and implement tricks and approximations from the free energy literature that move us along the “fast and accurate enough” tradeoff curve
• Help determine where more physics is needed and where we can safely approximate
• Build tools, not just papers
• Design, implement, and maintain free energy workflows and utilities that other scientists at Genesis can actually use
• Contribute production quality code, tests, and documentation
• Work with ML researchers and platform engineers to plug your methods into GEMS, our internal platform for molecular generation, and as well as our internal benchmarking suites
• Partner with ML, CADD, and medicinal chemistry
• Collaborate with ML researchers to combine data driven models with physics based methods, especially at the high potency end where physics is “the only game in town”
• Work with CADD and medicinal chemists to interpret free energy results and refine design hypotheses
• Help teams reason about convergence, error bars, and when to trust (or not trust) free energy outputs in real drug programs
• Drive impact within the first 90 days
• Quickly get hands on with our existing free energy related workflows and code.
• Propose and execute concrete improvements that shorten turnaround time, improve ranking at the top of the potency range, or make the tools easier to use for project teams.
• Start to define a roadmap for free energy at Genesis, including platform wide improvements and project specific ideas.

Requirements

• Experience with drug discovery or platform methods development.
• Strong track record in binding free energy method development for small molecules (for example FEP, TI, alchemical methods, QM/MM free energies, related approaches).
• Evidence that you have built a method or tool that others actually use: open source contributions, internal platforms, or widely used workflows.
• PhD in computational chemistry, theoretical chemistry, biophysics, chemical physics, or a related field, or equivalent experience.
• Proficiency in Python is a requirement, while experience with a compiled language (C, C++, Fortran, or similar) is a plus.
• Experience with modern software development best practices, especially git and test driven development.
• Comfortable diving into existing code, understanding design choices, and making careful modifications rather than always starting from scratch.
• Experience integrating methods with MD engines and workflow tools (for example OpenMM, GROMACS, NAMD, OpenFE, or similar ecosystems).

Tech Stack

• Open Source
• Python

Benefits

• We are proud to be an inclusive workplace and an Equal Opportunity Employer.