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Job Details

Merck & Co, Inc

Principal Scientist, Protein Engineering Machine Learning, Discovery Biologics

Engineering and Architecture

Architectural Engineering


Boston, Massachusetts, United States

Job Description

Discovery Biologics is seeking a Principal Scientist and group leader with experience in computational protein design and/or machine learning to support our biologics pipeline. At our company's Research Laboratories, we believe innovations at the intersection of machine learning, computational protein design, and HTP experimentation will transform the way we bring new therapies to patients. Our organization seeks to directly integrate computational and wet-lab researchers with state-of-the-art automation to accelerate the discovery, engineering, and characterization of novel biologics in the pre-IND pipeline. We are a highly diverse and collaborative group of researchers working at the edge of computation, disease biology, and biotherapeutics. We collaborate broadly within our Research Division, and with academic and industry partners to accelerate the pace of biologics discovery. We recognize that the diversity in our team is our strength, and we are committed to creating an inclusive environment for all employees. Successful candidates must demonstrate inclusive behaviors in working with a diverse group of researchers to drive our core mission.

The successful candidate will play a leading role to identify, develop and deploy cutting-edge computational and machine learning methods that will enhance design and engineering workflows in the Discovery Biologics pipeline. They will partner across Discovery Biologics, Data Science, and IT departments to implement foundational algorithms, and democratize the use of machine learning methods across Discovery Biologics programs. Optimal candidates will also have experience with, or a demonstrated passion for, biotherapeutic drug discovery and will be motivated by opportunities to co-lead drug discovery teams focused on engineering biologics molecules. As a project leader, they will set priorities and goals for their teams and work side-by-side with them to solve complex research problems. As a senior leader in the group, they will mentor, coach, and train group members. This is a highly multi-disciplinary role. The successful candidate will need to communicate effectively in diverse team environments spanning data science, machine learning, protein engineering, and preclinical developability. They will also need to regularly update senior leadership and clinical management. This role is central in providing vision and continuity across a diverse group of innovative researchers who are driving the next revolution in biologics discovery and engineering.

Minimum Education Requirements:

  • PhD in Computational Biology, Computational Chemistry, Structural Biology, Biochemistry, or a related discipline with demonstrated expertise in novel engineering methods including machine learning and 8+ years of industry experience; MS +10 or BS +14 years of experience

Required Experience:

  • Experience in the discovery, engineering, or development of biotherapeutics

  • Significant experience engineering biologics using protein modeling software (e.g. Rosetta, TrRosetta, MOE, GROMACs, or similar)

  • Fluency in at least one modern programming language such as C++, Python, or similar.

  • Experience leading teams to implement novel computational methods to solve complex research challenges

  • The desire to teach and educate wet-lab researchers on the fundamentals of computational protein modeling methods and machine learning

  • Excellent written and oral communication skills

  • A demonstrated passion for team building and a track record of talent development

  • A champion for diverse and inclusive cultures

Preferred Experience and Skills:

  • Computational prediction or de novo design of therapeutic proteins or antibodies (biophysical properties, humanization, CDR prediction, antibody docking, and language models with structural integration)

  • Development and implementation of protein machine learning methods using challenging datasets

  • Development and implementation of protein deep learning methods using neural networks (LSTM, Transformers, GNN, VAE, etc.)

  • Structure and/or sequence based featurization of protein macromolecules for machine learning

  • Molecular dynamics of protein molecules including statistical descriptions of protein ensembles

  • Protein-protein interaction prediction and molecular docking

Key Responsibilities

  • Develop and implement computational strategies to guide the design of biotherapeutics with desired biological and development characteristics.

  • Working with senior leaders and peers to set group strategy for machine learning adoption and implementation

  • Providing technical leadership for machine learning projects across Discovery Biologics

  • Present to group meetings, machine learning initiatives, and project and clinical teams

  • Co-lead of biologics drug discovery programs, including molecule design, registration and DNA construct ordering

  • Actively develops talent, strategically maximizes diversity to complement and strengthen their team

  • Fosters a high-performance culture of collaboration, engagement, self-accountability and inclusion

We are a research-driven biopharmaceutical company. Our mission is built on the simple premise that if we “follow the science” that great medicines can make a significant impact to our world. We believe that a research-driven enterprise dedicated to world-class science can succeed by inventing medicine and vaccine innovations that make a difference for patients across the globe.

Who we are …

We are known as Merck & Co., Inc., Rahway, New Jersey, USA in the United States and Canada and MSD everywhere else. For more than a century, we have been inventing for life, bringing forward medicines and vaccines for many of the world's most challenging diseases. Today, our company continues to be at the forefront of research to deliver innovative health solutions and advance the prevention and treatment of diseases that threaten people and animals around the world.

What we look for …

Imagine getting up in the morning for a job as important as helping to save and improve lives around the world. Here, you have that opportunity. You can put your empathy, creativity, digital mastery, or scientific genius to work in collaboration with a diverse group of colleagues who pursue and bring hope to countless people who are battling some of the most challenging diseases of our time. Our team is constantly evolving, so if you are among the intellectually curious, join us—and start making your impact today.


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If you have been offered a separation benefits package, but have not yet reached your separation date and are offered a position within the salary and geographical parameters as set forth in the Summary Plan Description (SPD) of your separation package, then you are no longer eligible for your separation benefits package. To discuss in more detail, please contact your HRBP or Talent Acquisition Advisor.


For positions located in the United States and Puerto Rico – Subject to applicable law, all new hires (including internal transfers) must demonstrate that they are fully vaccinated against COVID-19 or that they qualify for a medical or religious exemption to this vaccination requirement. New hires (including internal transfers) to a position that, as determined by the Company, requires routine collaboration with external stakeholders (such as roles in health services or customer-facing commercial or research-based roles) (“Customer-Facing Role”) who are not vaccinated must qualify for a medical or religious exemption and be in a position that the Company determines can accommodate unvaccinated employees without causing an undue burden to business operations. If, following dialog with the candidate as appropriate, it is determined that the candidate either a) does not qualify for a religious or medical exemption or, b) for candidates applying for Customer-Facing roles, it is determined that allowing the candidate to work without vaccination would cause an undue burden to the Company, the candidate will be ineligible for hire or transfer, or any offer of employment or transfer (if applicable) will be revoked. Please note that notwithstanding the approval of any reasonable accommodation, the Company reserves the right to monitor, modify, or revoke any such accommodation if it is determined, following dialog with the employee, that the accommodation is no longer effective or results in an undue burden to the Company.

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Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.

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Requisition ID:R200419