Computational Chemistry Senior Research Scientist

Vertex Pharmaceuticals • San Diego, CA

3d • Hybrid

About The Position

We are seeking a passionate and innovative Senior Research Scientist in Computational Drug Design to join our dynamic team at Vertex’s research site in San Diego, California. In this role, you will provide scientific leadership for computational chemistry efforts on active drug discovery programs, shaping design strategy and influencing compound prioritization through close partnership with medicinal chemists. You will leverage cutting-edge computational chemistry techniques to drive drug discovery efforts, from lead identification to optimization. Collaborating with interdisciplinary teams, you will apply your expertise in cheminformatics, molecular modeling, and data science to design and deliver transformative therapies. This is an exciting opportunity to contribute to the development of life-changing medicines while advancing computational capabilities within a global organization. This role also offers opportunities for growth toward increased scientific leadership, program ownership, and broader influence across Vertex’s computational drug discovery efforts.

Requirements

• Hands-on experience with a broad range of computational methods, including virtual screening, programming, statistics, data analysis, and ADME modeling.
• Proven expertise in applying molecular modeling methods to structure-based and/or ligand-based drug discovery.
• Deep knowledge of computational chemistry techniques, including FEP, ML, and QSAR.
• Proficiency with commercial and open-source molecular modeling and data mining software.
• Strong analytical and problem-solving skills, with the ability to manage multiple projects and priorities effectively.
• Excellent written and verbal communication skills, with a collaborative mindset.
• Ph.D. (or equivalent degree) in engineering, science or math and 2-5 years of productive, relevant post-doctoral employment experience with a broad range of computational methods, including virtual screening, programming, statistics, data analysis, and ADME modeling.
• Master's Degree (or equivalent degree) in similar fields and 5+ years of productive, relevant employment experience, or Bachelor's Degree (or equivalent degree) in similar fields and 8+ years of productive, relevant employment experience

Nice To Haves

• A track record of contributing to the development of innovative computational tools and methodologies.

Responsibilities

• Serve as a member of multidisciplinary drug discovery teams, working closely with medicinal chemists, structural biologists, and DMPK scientists to translate computational insights into actionable design hypotheses at our San Diego site and across Vertex’s global network to maximize the impact of computational approaches.
• Develop and apply state-of-the-art computational chemistry methods, including machine learning (ML) techniques, free energy perturbation (FEP), and other molecular modeling techniques to guide compound design, accelerate decision-making, and reduce experimental cycles.
• Design and implement innovative in-silico strategies to address critical challenges in drug discovery programs.
• Partner with the Computational Drug Design and Chemical Data Science teams to identify and integrate novel methodologies that enhance computational impact.
• Drive effective communication and collaboration across departments to ensure seamless integration of computational workflows into drug discovery pipelines.
• Contribute to the continuous improvement of computational tools and methodologies in collaboration with the global Data and Computational Sciences (DCS) group.

Benefits

• This role is eligible for an annual bonus and annual equity awards.
• From medical, dental and vision benefits to generous paid time off (including a week-long company shutdown in the Summer and the Winter), educational assistance programs including student loan repayment, a generous commuting subsidy, matching charitable donations, 401(k) and so much more.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Education Level: Ph.D. or professional degree
• Number of Employees: 1,001-5,000 employees