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Scientist I, Computational Chemistry

At Blueprint Medicines, as our name indicates, we are creating a blueprint for the future of healthcare.  We are a leading company in the personalized medicine revolution by focusing on delivering new medicines that are targeted to the genetic driver of disease.  We do this by leveraging our one-of-kind drug discovery platform to discover, develop and work to bring highly-selective kinase inhibitors to patients globally.  This prolific scientific platform has enabled Blueprint Medicine to build a pipeline of novel therapies that span three distinct areas of medicine; genomically defined cancers, rare diseases and cancer immunotherapy.

To aid in our mission of rapidly developing highly selective compounds to address clear genomic drivers of disease, we are seeking a motivated scientist with expertise in computational chemistry to join our Drug Discovery team. In this role, the ideal candidate will integrate and apply advanced computational chemistry techniques like free energy perturbation, analysis of water energetics, and molecular dynamics simulations to support project teams across all stages of drug discovery. You’ll be an integral part of the chemistry and the broader drug discovery team.


  • Provide computational chemistry support to on-going drug discovery projects using a broad spectrum of structure-based drug design and cheminformatics techniques and analyses
  • Evaluate and implement advanced binding free energy workflows, including free energy perturbation, to enable molecule design
  • Apply molecular dynamics and other simulation techniques to understand protein flexibility, structural differences between on- and off-targets, and molecular recognition of small molecule inhibitors  


  • PhD in computational chemistry, biophysics, physics or related fields
  • Ideal candidate has post-doctoral experience and/or 2+ years of work experience in a drug discovery setting
  • Strong scientific background and proven high levels of performance, as evidenced by driving projects to key milestones and a strong publication record.
  • Demonstrated experience in the application of binding free energy calculations and molecular dynamics simulations to understand molecular recognition and biomolecular processes
  • Demonstrated experience in complex problem solving through in depth analysis of data


  • Excellent communication skills. Ability to communicate in an open, clear, timely and consistent manner
  • A results-driven mindset with analytical and problem-solving skills
  • Desire to work as a team member in a dynamic, fast-paced biotech environment and contribute to the development of the next generation of kinase inhibitors
  • Experience with Schrodinger and KNIME software a plus
  • Knowledge of structural features of kinases a plus

All applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability or protected veteran status.


Blueprint Medicines’ mission is to dramatically improve the lives of patients with genomically defined diseases. Our singular focus is to use our deep understanding of the genetic blueprint of cancer and other diseases driven by the abnormal activation of kinases to craft highly selective medicines aimed at eradicating these diseases.

We don’t think in small steps. We think in giant leaps.

We are driven by the pursuit of new ideas, new innovations, and new ways of thinking.

We know that what each and every one of us does matters and that our success depends on our ability to work together. We believe we are at our best as a company when our employees are thriving and foster a culture that provides opportunities to grow and develop professionally, while also having fun.

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