Senior Principal Research Scientist, Physics-Based Methods Development

Job Description

We are seeking a highly motivated and experienced Computational Chemist to join our Data and Computational Sciences Group in Boston to lead scientific innovation in physics-based molecular modeling and simulations. As a recognized expert and thought leader, you will develop the company’s physics-based computational methods platform: prototype, benchmark, and implement computational methodologies, collaborate with software engineers to scale solutions across with organization, collaborate with other scientists to establish best practices, and drive global alignment to accelerate drug discovery. This is a highly visible, scientifically influential role with broad impact across multiple therapeutic areas.

This is a Boston based, hybrid position requiring 3 days/week onsite.

Key Responsibilities:

• Develop, implement, and optimize advanced physics-based methods including:
  • Alchemical and endpoint free energy methods (e.g., FEP, MM/GBSA) for potency, selectivity, and optimization.
  • High-performance molecular dynamics (MD) and enhanced sampling (e.g., metadynamics, REST) to explore conformational landscapes and transitions.
  • Refinement of artificial intelligence derived protein structures to resolve ambiguous or flexible regions and preparation of active site-ready structures for reliable docking.
  • Virtual screening workflows using physics-based docking and scoring.
  • Model complex drug modalities beyond Ro5 such as peptides with conformational constraints and challenging permeability profiles.

• Collaborate with ML/AI scientists and computational chemists to evaluate and implement ML enabled physics-based methods
• Serve as a technical and scientific SME, influencing both strategic direction and day-to-day execution.
• Work with scientific engineers to ensure high-performance physics-based platforms are robust and accessible from cloud and on-prem compute resources.
• Proactively seek opportunities to enhance Vertex’s global R&D efforts through cross-functional collaboration with Structural Biology, and Data Science teams
• Stay at the forefront of computational chemistry innovations, proactively incorporating emerging tools and technologies to enhance team capabilities
• Mentor and guide junior scientists, fostering a culture of innovation, collaboration and scientific excellence

Skills and qualifications required:

• Ph.D. in Computational Chemistry, Biophysics, Chemical Physics, or related field with 6+ years of post-Ph.D. experience in biotech, pharma, or academic research or Master's and 9+ years, or Bachelor's and 11+ years
• Expertise in free energy methods, molecular simulations, and computational drug design.
• Demonstrated experience in developing methods with successful impact in translating to real-world drug discovery. Deep understanding of protein-ligand interactions, and membrane systems.
• Fluency with simulation packages (e.g., AMBER, GROMACS,,) and familiarity with common toolkits such as OpenMM, OpenFF
• Strong software development skills in Python, and C/C++ and scripting (Python, Bash, etc.) and familiarity with modern software development practices
• Excellent leadership, communication and decision-making skills, fostering collaboration across teams

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Pay Range:

Disclosure Statement:

Flex Designation:

Flex Eligibility Status:

In this Hybrid-Eligible role, you can choose to be designated as: 
1.    Hybrid: work remotely up to two days per week; or select
2.    On-Site: work five days per week on-site with ad hoc flexibility.

Note: The Flex status for this position is subject to Vertex’s Policy on Flex @ Vertex Program and may be changed at any time. 
 

Company Information

Vertex is a global biotechnology company that invests in scientific innovation.

Vertex is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry, ethnicity, disability, veteran status, genetic information, sexual orientation, marital status, or any characteristic protected under applicable law. Vertex is an E-Verify Employer in the United States. Vertex will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law.

Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should make a request to the recruiter or hiring manager, or contact Talent Acquisition at [email protected]