Silicon Therapeutics


Silicon Therapeutics is building an exceptional team of outstanding life scientists and computer scientists with a unifying belief that we can make better medicines using computers. We foster a collaborative, respectful, and flexible work environment that allows individuals to thrive. Our supportive and open work environment enhances synergies among individuals, thereby maximizing the quality and efficiency of our efforts. We embrace diversity and value different perspectives, ideas, and identities of everyone on the team.

 Silicon Therapeutics, a Boston-based integrated drug discovery company, is looking for drug designers interested in applying advanced computational approaches to structure-based drug discovery projects. Our science, our team, and our mission are focused on developing and applying cutting-edge simulation methods to progress our R&D pipeline of innovative medicines for patients.


  • At Silicon Therapeutics, the molecular modeler/designer broadly influences and impacts projects from early target assessment and druggability, through compound design and optimization, into preclinical development.
  • The qualified individual will serve as an inspirational and scientific leader at the apex of internal design teams, and is responsible for:
    • Driving our R&D projects toward the clinic
    • Working with computational scientists and synthetic chemists to interpret structural information and proactively suggest new design ideas.
    • Maintaining a high-level understanding of project and asset deliverables, and the ability to translate this into design hypotheses and goals using structural information.
    • Understanding our internal physics-based simulation capabilities and applications thereof.
    • Interactingwith the simulation platform team to interpret fidelity and accuracyof computational calculationsto continuouslymodify / improve internal applications.
    • Maintain and develop working knowledge of contemporary computational chemistry methods and their use in molecular design and data analysis as applied to drug design projects.


  • A broadly experienced computational chemist¬†with the ability to interpret and communicate structural information to chemists and proactively suggest ideas within a routine design cycle, that support compound optimization goals.
  • Expert level knowledge in structure-based drug design (SBDD), ligand conformation, protein structure and function, and protein- ligand interactions.
  • 7+ years of pharma experience working at the interface of chemistry and computational sciences to support compound design and project advancement through lead optimization.
  • Hands-on experience with several modern molecular modeling techniques (docking, molecular simulation, homology modeling, quantum mechanics, ligand- and structure-based design.
  • Strong understanding of all aspects of modern drug discovery including medicinal chemistry, multi-parameter optimization, DMPK principles, etc.
  • Knowledge of fundamental chemistry principles, nomenclature, biosteric replacements and common transformations that enable rational SBDD in a design team.
  • High level understanding of how compound design / chemistry integration supports project teams goals, timelines and deliverables.
  • Experience Strong communication and collaboration skills with ability to work well in multidisciplinary environment
  • Ph.D. in medicinal chemistry, organic chemistry, or related field as well as a track record of technical excellence as shown by peer reviewed publications and inventorship status on patents
  • Proficiency in scientific programming (e.g. Python, R, C++, Fortran)
  • Proficiency in molecular simulations packages (e.g.NAMD, OpenMM, Gromacs, LAMMPS)
  • Experience and understanding of physics-based computational approaches (FEP, MD, QM)


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