Senior Scientist, Cheminformatics

Our Company is currently seeking an exceptional, highly motivated Senior Scientist, Cheminformatics to join the Modeling & Informatics group within Discovery Chemistry. The successful candidate will join multidisciplinary discovery teams to drive the development and application of advanced cheminformatics workflows, machine learning models, and data-driven methods. This role focuses on accelerating drug discovery pipelines across both small molecules and emerging modalities—such as cyclic peptides, macrocycles, and DNA-Encoded Library platforms—in close partnership with computational and medicinal chemists.

·         Computational Chemistry Partnership: Partner closely with computational and medicinal chemists on Discovery Chemistry project teams to address challenging structure-activity relationships and multi-parameter optimization

·         Emerging Modalities & DNA-Encoded Library Informatics: Develop and deploy specialized informatics workflows for non-traditional modalities (cyclic peptides, macrocycles) and DNA-Encoded Library platforms, including combinatorial enumeration, selection data triage, and hit prioritization.

·         Workflow & Algorithm Development: Design, validate, and implement scalable cheminformatics and machine learning pipelines for predictive property modeling, virtual screening, and chemical library triage.

·         Data Infrastructure & Tooling: Establish robust, automated computational tools and data pipelines that bridge internal chemical data platforms and modern modeling frameworks.

·         Scientific Presence & Mentorship: Maintain an active external scientific presence through publications, conference presentations, and community engagement, while mentoring junior staff, interns, and co-ops.

·     Ph.D. (or close to completion) in Cheminformatics, Computational Chemistry, Chemistry, Computer Science, Bioinformatics, or a related quantitative discipline; OR    

·         M.S. degree with 4+ years of relevant industry/research experience.

·         Demonstrated expertise in cheminformatics fundamentals (molecular representations, fingerprints, similarity search, tautomer enumeration, and conformer generation).

·         Strong programming proficiency in Python and scientific computing libraries (NumPy, SciPy, Pandas, scikit-learn).

·         Extensive hands-on experience with modern cheminformatics toolkits (e.g., RDKit, OpenEye Toolkits, or CDK).

·         Experience developing and validating machine learning or statistical QSAR models applied to chemical or biological data.

·         Demonstrated track record of effective collaboration in multidisciplinary scientific teams.

·         Strong oral and written communication skills, evidenced by peer-reviewed publications or presentations.

·         Experience with computational design of cyclic peptides, macrocycles, or non-canonical peptide representations (e.g., HELM notation).

·         Experience with DNA-Encoded Library analysis, combinatorial enumeration, or NGS selection data deconvolution.

·         Familiarity with molecular modeling and structure-based design tools (e.g., Schrödinger, MOE) to facilitate cross-talk with molecular modelers.

·         Experience deploying containerized workflows (Docker), version control (Git), and utilizing Linux/high-performance computing (HPC) environments.

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Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.  As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

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The primary location for this posting is:

Where required by law, the compensation range for this role is provided below.

The salary range for the primary location of this role is:

This range reflects the Company's reasonable expectation of the base salary applicable to this role at the time of posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs. The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits. Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits.