Scientist / Senior Scientist, Structure-Based Modeling

Overview

Scientist / Senior Scientist, Structure-Based Modeling at Deep Origin is seeking a Scientist or Senior Scientist with strong expertise in structure-based drug design, including docking, molecular dynamics (MD), and free energy perturbation (FEP), to support a transformative ARPA-H initiative. You will lead the design of robust simulation workflows and analyze protein-ligand structures across a large target panel to support predictive modeling for therapeutic discovery.

Responsibilities

• Analyze tens to hundreds of protein targets relevant to ADMET and off-targets, focusing on conformations, binding site flexibility, and ligand-bound states to guide structure preparation and ensemble design;
• Run and refine docking, MD, and FEP (RBFE and ABFE) simulations using state-of-the-art tools;
• Apply methods such as restraints, alchemical transformations, and sampling strategies to ensure robust and reproducible FEP workflows...