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Principal Scientist - Computational Chemistry

Novo Nordisk
Lexington, MA
Start date
Apr 20, 2024

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Science/R&D, Biotechnology, Chemistry
Required Education
Position Type
Full time
Genetown, Best Places to Work

Job Details

About the Department                                                                                                                                             

Computational Drug Design (CDD) is the Novo Nordisk organization where we develop and apply state of the art capabilities in data science, predictive modeling, and AI/ML to enable both ligand and structure-based drug design. Scientists within CDD collaborate seamlessly with teams across the globe to invent better molecules faster. With an unbiased approach to drug modalities, in-house access to the newest screening techniques, and world-class experimentation, we have a wealth of opportunities to impact our pipeline and save and improve patient lives. We work in multidisciplinary, highly collaborative discovery teams both locally and across Novo Nordisk’s global network to invent novel medicines by applying advanced computational techniques and developing innovative computational methods. We engage in external collaborations to ensure access to innovative research and technology. 

Small Molecule Digital Chemistry (SMDC) is dedicated to the research and development of small molecule therapeutics. Our role is two-fold: support cutting-edge pharmaceutical research projects and develop innovative computational technologies in digital chemistry field. To be successful, we foster strong collaborations with Small Molecule Medicinal Chemistry within our Global Research and Technology (GRT) organization and colleagues across the Data Science and Innovation (DSI) organization. Our mission is to deliver in silico models, cheminformatics tools and computational chemistry platforms to enable in silico small molecule drug design to benefit patients across the globe.

We believe in the value of a diverse and inclusive culture. Together, we build and grow talent to ensure the development of novel solutions. The team is comprised of collaborative, diverse and passionate people who have a true sense of pride in their work.  We are committed to helping each other grow, and we are driven by the opportunity to make a difference in the lives of people living with chronic disease. Everything we do starts and ends with the patient. And, while changing the future of chronic disease treatment, such as diabetes and obesity, is no easy task, we also recognize the importance of an enjoyable workplace, which is why we have cultivated a culture of fun, ingenuity, and innovation. Our competitive compensation package and support of a healthy work-life balance all add to a best-in-class employee experience. 


The Position

The Principal Data Scientist – Computational Chemistry will contribute to the Small Molecule Digital Chemistry team's effort towards exploring, implementing, and applying computational chemistry methods and tools to achieve CDD goals. The Senior/Principal Data Scientist – Computational Chemistry will have knowledge and experience in advanced molecular modeling and computational drug design methods as well as small molecule project support. They will have a high degree of proficiency in modern 3D modeling tools for structure and ligand-based drug design, scientific programming, machine learning methods, and HPC/cloud computing. They will engage in drug discovery projects from early discovery to scale up and lead the development of complex workflows to prepare structural data, generate 2D/3D models, execute virtual screening, and perform small molecule design and optimization. The Senior/Principal Data Scientist – Computational Chemistry will champion an in-silico first mindset and show initiative in recognizing and addressing unmet scientific needs using internal and external data



This position reports to the Senior Scientific Director of SMDC. They will have close interactions with scientists and experts within Medicinal Chemistry, Quantitative Biology and ADME & Tox. Additional internal partners include data scientists, data engineers, ML specialists, software developers and others across US, UK, and Denmark. External relationships include commercial and academic collaboration partners.


Essential Functions

  • Advance Small Molecule pharmaceutical project portfolio through computational chemistry method applications
  • Develop digital chemistry processes and workflows to address pharmaceutical project needs. 
  • Conceptualize approaches, identify capability gaps, and set goals within small molecule drug design. 
  • Represent Small Molecule CDD as a technical/scientific lead on cross-functional research teams that include discovery, development, and research IT organizations 
  • Prepare and present research in top-leading journals or conferences.  
  • Maintain a well-documented, reusable codebase, and traceable model history  
  • Maintain scientific and technical expertise through familiarity with scientific literature and attending conferences.  
  • Provide pharmaceutical project teams with computational strategies to inform, influence, and prioritize designs for potency/selectivity and improve ADME/Tox endpoints
  • Work closely with Therapeutic areas, Research Chemistry and Computational Drug Discovery to drive discovery and development efforts  
  • Work with ML scientists and engineers to guide the development of our ML model infrastructure. 
  • Collaborate with colleagues from ADME, Tox, Computational Drug Discovery and ML to implement production quality global and local predictive models. 
  • Actively participate in virtual global team meetings regularly 
  • Participate in the evaluation of external and internal capabilities and facilitate collaborations with external partners 
  • Present results to interdisciplinary teams of experimental, modeling scientists and machine learning colleagues at company meetings.


Physical Requirements

Up to 10% overnight travel required.



  • Masters degree with 10+ years required  
    • Ph.D. with 8+ years of relevant experience can be considered. Degree in Cheminformatics, Computational Chemistry, Computer Sciences or related quantitative preferred
  • Relevant experience includes:
    • Research experience in the field of small molecule drug discovery within industry or academia (industry preferred) as demonstrated by publications or presentations documenting impactful application of computational chemistry methods.
    • Proficiency in general molecular modeling techniques (e.g. docking, molecular dynamics simulations, pharmacophore search, structure/ligand-based design).
    • Hands on experience with molecular modeling software (e.g. Maestro, OpenEye, Rosetta, etc.) and cheminformatics packages (e.g. RDKit)
    • Familiarity with QSAR/QSPR modeling, cheminformatics, and AI/ML methods.
    • Proficiency in scripting or programming languages such as Python or C++
    • Ability to perform in-depth data analysis and develop algorithms to solve complex problems
    • Excellent written and oral communication skills, including ability to present to diverse audiences 
    • Detail oriented with strong documentation skills
  • Preferred experience: 
    • Familiarity and working experience with a breadth of tasks of the Design-Make-Test-Analyze drug discovery cycle – highly preferred
    • Working experience with Linux and HPC environments.



We commit to an inclusive recruitment process and equality of opportunity for all our job applicants.


At Novo Nordisk we recognize that it is no longer good enough to aspire to be the best company in the world. We need to aspire to be the best company for the world and we know that this is only possible with talented employees with diverse perspectives, backgrounds and cultures. We are therefore committed to creating an inclusive culture that celebrates the diversity of our employees, the patients we serve and communities we operate in. Together, we’re life changing.


Novo Nordisk is an equal opportunity employer. Qualified applicants will receive consideration for employment without regard to race, ethnicity, color, religion, sex, gender identity, sexual orientation, national origin, disability, protected veteran status or any other characteristic protected by local, state or federal laws, rules or regulations.


If you are interested in applying to Novo Nordisk and need special assistance or an accommodation to apply, please call us at 1-855-411-5290. This contact is for accommodation requests only and cannot be used to inquire about the status of applications.


Novo Nordisk is a leading global healthcare company, founded in 1923 and headquartered in Denmark. Our purpose is to drive change to defeat diabetes and other serious chronic diseases such as obesity and rare blood and endocrine disorders. We do so by pioneering scientific breakthroughs, expanding access to our medicines, and working to prevent and ultimately cure disease. Novo Nordisk employs about 54,400 people in 80 countries and markets its products in around 170 countries. For more information visit

Our US Research & Development hub, located in the Greater Boston area, brings together the best talent to drive life science innovation. Located in Lexington, Watertown and Cambridge, our teams reflect the full scope of R&D, from early research through late-stage clinical development. We are building for the future by creating a distinct R&D community based on collaboration, partnerships, and cutting-edge research across multiple modalities and therapeutic areas. We recognize that improving human health starts here and that patients rely on us. By combining the speed and agility of biotech with the quality, resources, and stability of a large pharmaceutical company, our US R&D hub will benefit from the best of both worlds to develop new medicines that meet the needs of patients.


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