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Senior/Principal Scientist - Computational Chemist (SF Bay Area)



South San Francisco, CA, USA
Posted on Wednesday, February 7, 2024

Vilya is a computational biotechnology company creating a novel class of medicines to precisely target disease biology. We believe computational approaches are an integral, if not foundational, component of drug discovery and development. Our platform is built on ground-breaking research in advanced computational approaches and taps into uncharted chemical space to design new molecular structures not found in nature.

We are harnessing the power of our platform to go after previously impossible targets in an array of indications. Vilya’s ultimate goal is to solve some of the most challenging unmet medical needs that exist today.

Our Vision: Harness a revolution in technology and biology to better human health

Our Mission: Build an independent, leading biotech company founded on intelligent drug design to cure the incurable

We are seeking a Senior/Principal Scientist - Computational Chemist to drive drug design with state-of-the-art machine learning and physics based methods in a fast-based and early-stage, future-looking company that is championing an in silico-driven drug discovery process.


  • As a part of a cross-functional team of experimental and computational scientists, utilize state-of-the-art in silico tools to improve and predict affinity, selectivity, ADME, and safety of next-generation peptide therapeutics.
  • Apply our proprietary deep learning and physics-based methods to lead optimization.
  • Lead design meetings on multiple targets.
  • Evaluate and promote novel methods found in the fast-moving literature.
  • Help shape an exciting and growing “in silico driven” scientific culture.


Demonstrated ability to…

  • Drive small molecule, oral drug design toward improving affinity, selectivity, ADME, Safety constrained by chemical synthesis knowledge.
  • Execute structure-based and ligand-based design, including docking and pharmacophore/shape-based virtual screening.
  • Perform molecule dynamics simulations, including relative or absolute binding free energy calculations.
  • Assess structure-activity and property-activity relationships, and translate these learnings into constraints for design.
  • Assess experimental protein structures, including receptor druggability, dynamics, selectivity, and solvation.
  • Predict small-molecule binding versus non-binding using Free Energy Perturbation (FEP).
  • Evaluate strain energy using physical-chemical knowledge or quantum-mechanical calculations.
  • Curate training sets for machine learning (ML) models as well as evaluate and apply these models using statistical analysis.
  • Communicate design ideas to the broader chemistry and drug discovery teams.
  • Understand protein biochemistry and disease pathway implications.
  • Develop complex drug-design and data analysis workflows via scripting, ideally in Python and modern data analysis packages (Pandas, numpy, Jupyter)
  • Liaison with software companies, propose and drive feature enhancements.
  • Have good collaboration skills and can work well in a cross- functional environment.

Additional experience as a plus…

  • Peptide drug discovery
  • Computational chemistry utilizing cloud computing
  • Building and applying machine learning / deep learning models
  • Development of novel tools and automation using Python utilizing current software development source code control and testing strategies.


  • Opportunity to work in a disruptive startup with a talented, experienced, and growing team of dedicated individuals
  • 401(k) plan with employer matching for contributions
  • Stock options
  • Excellent medical, dental, and vision coverage
  • Open, flexible vacation policy
  • Support to attend professional conferences that are meaningful to your career growth
  • Monthly cell phone reimbursement
  • Commuter benefits
  • Salary Range : $165,000 - $205,000.