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Co-op Computational Chemistry

Semma Therapeutics

Semma Therapeutics

San Diego, CA, USA
Posted on Thursday, September 28, 2023

Job Description

The Vertex Co-op Program offers students the opportunity to learn about the pharmaceutical industry from a hands-on perspective. You will be working closely with and learning from some of the brightest people in the industry. When you join our co-op program you should not be surprised to see that our environment is one that is innovative and team oriented, where collaboration is not just a word, and "we are relentless" is in everything we do. Students can expect to be challenged by their project plan, connect with other co-ops, and feel valued by the Vertex community. Not only will co-ops learn about their day-to-day tasks through their specific work assignments, but they will interact and have exposure to our organizational leaders and their teams.

Job Summary:

We are looking for exceptional candidates to assist with early stage research on active drug discovery programs at Vertex in San Diego. The project will entail application of physics-based simulation techniques in lead optimization programs. No prior experience working in industry is required.

The Computational Chemistry group uses methods encompassing all aspects of drug discovery—from quantum calculations to empirical and knowledge-based models—to accelerate the discovery, prioritization, and analysis of high-quality drug candidates.

Key Responsibilities:

  • The candidate will be expected to perform computational experiments to test hypotheses and develop models
  • The candidate must have the ability to work independently and as part of a team
  • The candidate must be assertive and ask questions when uncertain
  • The candidate should be able to develop and implement data analyses
  • The candidate will be required to regularly present their progress in formal and informal settings to colleagues
  • The candidate will interface with colleagues in other departments, such as DMPK, Medicinal Chemistry, Scientific Computing, or Structural Biology, as dictated by the project

Deliverables could include the deployment of molecular dynamics simulation and analysis workflows that enable evaluation of hypothesis backed by data.


  • Ph.D. students in computational chemistry or a related STEM field (chemistry, physics, computer science, structural biology) highly preferred
  • Experience with scripting (Python is preferred but Perl, R, Bash, or another language is acceptable)
  • Strong work ethic with excellent scientific skills
  • Strong oral and written communication skills
  • Molecular dynamics (MD) simulations (AMBER, OpenMM, or other programs)
  • Enhanced sampling techniques (metadynamics, umbrella sampling, or other methods)
  • Scientific toolkits for chemistry or simulations (CPPTRAJ, RDKit, OpenEye, or others)
  • Free energy calculations (FEP+, double decoupling, pathway-based methods, or other tools)
  • QSAR or other structure-activity model building
  • Statistics
  • Legally authorized to work in the United States
  • Candidate must be enrolled in an advanced degree program if graduating in January 2024

Pay Range $30.00 – $50.00 USD/hour

This job posting is for a temporary role with a third-party agency partner that provides services to Vertex. The individual selected for this role will be offered the role as an employee of that third-party agency; compensation, medical benefits, fringe benefits and other terms and conditions of employment shall be presented by the third-party agency upon offer. The range provided is a reasonable estimate for the pay range for this job at the time of posting. Some roles may also be eligible for overtime pay, in accordance with federal and state requirements. The actual pay rate will be based on a number of factors, including skills, competencies, experience, and other job-related factors permitted by law.

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