Director, Computational Chemistry at RAPT Therapeutics
South San Francisco, CA, US

PURPOSE OF JOB:          

RAPT Therapeutics is seeking a leader in Computational Chemistry who can improve the effectiveness of our drug discovery engine to deliver oral small molecule candidates for inflammatory diseases and cancer. This position will build out, develop, and optimize our computational chemistry capabilities and disciplines including, structure-based drug design and AI/ML to deliver compelling drug-like novel chemical matter. This position will report to the SVP of Drug Discovery and Preclinical Development and work closely with our Medicinal Chemistry, DMPK and Computational Biology teams. 

  • Will be responsible for identifying and deploying best practices in computational chemistry
  • Assessing where this discipline can be employed with greatest impact.
  • Supervise and manage a computational chemistry group and provide advice to others working with this technology



  • Lead the effective selection, development, and deployment of a suite computational chemistry techniques across RAPTs discovery portfolio
  • Assess current Computational Chemistry software and provide recommendations for improving effectiveness and utility of our drug design tools
  • Keep aware and implement new trends and tools in AI, machine learning and computational chemistry
  • Have oversight of the chemo-informatics aspects of Dotmatics and recommend software that could leverage our data in this database.
  • Work with medicinal chemists and biologists to assess potential targets for small molecule binding sites
  • Deploying virtual screening for the identification of novel chemical matter when appropriate
  • Facilitate appropriate use of cheminformatics to triage virtual and wet screens and to analyze RAPT’s discovery compounds
  • For projects in lead optimization and beyond, recommend and facilitate appropriate molecular modeling efforts including structure-based drug design workflows or development of pharmacophore models as necessary
  • Develops strong internal relationships with medicinal chemists to facilitate the design of molecules that specifically interact with their target and are likely to have good overall pharmaceutical properties
  • Identify and appropriate AI/ML tools to enhance RAPT’s analysis of project data and identify actionable insights
  • Build strong relationships across the Discovery group to foster innovative use of computational chemistry techniques across projects



  • D. in computational chemistry, biophysics, physical organic chemistry, statistical modeling, or ML/AI with 7 years experience in computational chemistry or a masters degree with 10+ years of experience in computational chemistry


  • Demonstrated expertise in structure-based drug design (SBDD), which includes molecular docking, pharmacophore models, virtual screening, molecular dynamics simulations and related techniques for protein-ligand interaction calculations.
  • Experience with ligand-based modeling, including QSAR methods, small molecule conformational analysis and 3D overlays
  • Expertise with protein modeling, such as ab-initio structure prediction, hot spot analysis and molecular dynamic modeling of proteins
  • Extensive experience with computational chemistry software such as Schrödinger, Cresset, Dotmatics, Vortex and Data Warrior
  • Understanding of how to design machine learning models that can effectively predict
  • Experience supervising/mentoring other computational chemists


California law requires pay information in job postings. The specific rate will depend on the successful candidate’s qualifications, prior experience, and other relevant factors. The estimated annual pay range for this position is $215,600 (entry-level qualifications) to $228,900 (highly experienced).