Our multi-disciplinary Research and Development organization combines state-of-the-art resources with world-class expertise in therapeutic discovery and development. We are inspired by the belief that a research-driven enterprise dedicated to scientific excellence can create medicines and vaccines that save and improve lives. Grounded in a culture of respect, invention, and collaboration, our organization offers a dynamic environment where you can build on a proud legacy of scientific breakthroughs while advancing your career.
Modeling and Informatics (M&I) is an inclusive group of approximately 50 computational chemists and data scientists within our global Discovery Chemistry organization. With a strong track record of pipeline impact, we apply cutting-edge capabilities in structure-based modeling and predictive science to advance drug design and development worldwide. With an unbiased approach to drug modalities, in-house access to the newest screening techniques, and world-class medicinal chemistry, we have a wealth of opportunities to impact our pipeline and ultimately save and improve patient lives.
We are seeking an exceptional, highly motivated computational scientist to join our Research Laboratories in South San Francisco, California. The ideal candidate combines strong interpersonal and problem-solving skills with deep expertise across AI/ML, computer science, biophysics, and computational chemistry, alongside a passion for applying innovative methods to complex scientific challenges. This role focuses on building algorithms, tools, and workflows that integrate predictive modeling, agentic scientific reasoning, and physics-based insight. The successful candidate will contribute to next-generation systems that reason across miltiple data sources, critically evaluate molecular hypotheses, and continuously learn from experimental feedback throughout the Design-Make-Test-Analyze (DMTA) cycle.
Responsibilities
Develop novel AI/ML algorithms and computational methods for representation, prediction, generation, reasoning, and decision-making, including methods that can serve as components of AI co-scientist and autonomous molecular-design systems.
Rigorously evaluate AI/ML methods against appropriate computational and experimental benchmarks, with an emphasis on scientific validity, uncertainty, robustness, appropriate baselines, failure modes, and prospective utility.
Develop and apply modern deep-learning approaches for molecular discovery that combine machine learning with physical and biophysical understanding of molecular systems, including molecular interactions, conformational energetics, thermodynamics, kinetics, solvation, molecular recognition, and structure-function relationships.
Develop agentic workflows that integrate predictive models, scientific tools, experimental data, simulations, structural information, SAR, and scientific literature to generate and critically evaluate molecular hypotheses.
Collaborate directly with medicinal and computational chemistry project teams to apply AI/ML and computational approaches to molecular design, SAR interpretation, hypothesis generation, and experimental prioritization.
Build reproducible scientific methods and workflows, pilot new approaches on active drug-discovery programs, and collaborate with colleagues to deploy successful methods across computational environments and integrate them into broader discovery platforms.
Conduct innovative research in computational chemistry, computer science, biophysical chemistry, and molecular modeling relevant to drug discovery, and contribute to the internal and external scientific community through publications and presentations.
Mentor scientists and help expand organizational capabilities in data-driven molecular design, computational methodology, and scientific reasoning.
NOTE: This role involves in-person collaborations and is an on-site position located at our research laboratories in South San Francisco, CA. This is NOT a remote role.
Requirements
Education:
Bachelor’s (with 7+ years), Master’s (with 4+ years) or Ph.D. (or Ph.D. completion by June 2027 ) in Engineering, Computer Science, Machine Learning, Chemistry, Computational Chemistry, Biophysics, Applied Mathematics or a related discipline and relevant experience.
Required Experience and Skills:
A minimum of two years of hands-on experience (or experience obtained during education) developing, training, and evaluating deep-learning models using a deep-learning framework (such as Pytorch, JAX, or similar).
Broad competency in modern data science.
Research experience applying the deep learning approaches to chemistry or biophysics problems.
Experience with agentic AI frameworks.
Track-record of scientific publications in peer-reviewed journals.
Strong Python skills for scientific programming, methods development, and algorithm development on Linux high performance compute.
Excellent written and oral communication skills.
Preferred Experience and Skills:
Experience with modern AI/ML methodologies relevant to molecular design such as graph neural networks, transformers, diffusion models, generative modeling, reinforcement learning, active learning, or molecular foundation models.
Experience with agentic AI frameworks such as LangChain, LangGraph, or similar.
Experience with cheminformatics, including tools such as RDKit.
Experience with 3D molecular modeling and physics-based computational methods such as protein-ligand modeling, structure-based molecular design, molecular dynamics, or quantum chemistry.
Scientific software-engineering experience, including translating research algorithms into robust, reproducible computational workflows.
Experience collaborating directly with experimental scientists.
EligibleforERP
Required Skills:
Agentic AI, Applied Mathematics, Artificial Intelligence (AI), Chemistry, Computational Chemistry, Data Modeling, Data Science, Deep Learning, LangChain (FrameWork), LangGraph, Linux, Machine Learning (ML), Molecular Modeling, PyTorch
Preferred Skills:
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The primary location for this posting is:
USA - California - South San Francisco (Grand Ave)
Where required by law, the compensation range for this role is provided below.
The salary range for the primary location of this role is:
$159,600.00 - $251,200.00
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 .
Additional location(s): Please note the salary range above applies to the Primary Location of the position. Where a role has other listed locations, different compensation guidelines may apply. You may find the salary ranges for additional locations below. If the salary range is not listed for the location you are applying to, our Talent Acquisition team will provide further information to you relevant to your location.
Additional location(s) Compensation Information:
San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance
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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.
Employee Status:
Regular
Relocation:
Domestic/International
VISA Sponsorship:
Yes
Travel Requirements:
10%
Flexible Work Arrangements:
Not Applicable
Shift:
1st - Day
Valid Driving License:
No
Hazardous Material(s):
N/A
Job Posting End Date:
11/19/2026
A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.