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Senior Molecular Modeling Jobs (NOW HIRING)

CEDENT

Senior Scientist

Branford, CT · On-site

$90K - $123K/yr

We're hiring a Senior or Principal Scientist to join our Biotherapeutics team's collaborative group ... Working knowledge of structure-activity relationships and/or molecular modeling is a plus

CEDENT

Senior Scientist (Branford, CT)

Branford, CT

$90K - $123K/yr

We're hiring a Senior or Principal Scientist to join our Biotherapeutics team's collaborative group ... molecular modeling is a plus Experience with mammalian expression systems (e.g., CHO/HEK), cell ...

Cedent

Senior Scientist (Branford, CT)

Branford, CT · On-site

$90K - $123K/yr

We're hiring a Senior or Principal Scientist to join our Biotherapeutics team's collaborative group ... Working knowledge of structure-activity relationships and/or molecular modeling is a plus

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Senior Molecular Modeling information

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$80.3K

$163.5K

How much do senior molecular modeling jobs pay per year?

As of Jul 6, 2026, the average yearly pay for senior molecular modeling in the United States is $80,287.00, according to ZipRecruiter salary data. Most workers in this role earn between $41,500.00 and $103,000.00 per year, depending on experience, location, and employer.

What are some typical challenges faced by Senior Molecular Modeling professionals in cross-functional research teams?

Senior Molecular Modeling professionals often work closely with medicinal chemists, biologists, and data scientists, which can present challenges in translating complex computational findings into actionable insights for diverse teams. Balancing multiple project priorities and adapting modeling techniques to evolving research goals are common hurdles. Strong communication skills and a collaborative mindset are essential to bridge gaps between computational and experimental perspectives, ensuring that modeling results effectively guide experimental design and decision-making.

What does a Senior Molecular Modeler do?

A Senior Molecular Modeler is a specialist who uses computer simulations and theoretical chemistry techniques to study and predict the structure, properties, and behavior of molecules. They often work in pharmaceutical, biotechnology, or materials science settings, helping to design new drugs or materials by modeling interactions at the molecular level. Their responsibilities include running simulations, analyzing data, developing new modeling methods, and collaborating with experimental scientists to interpret results. Senior roles also typically involve project leadership and mentoring of junior colleagues.

What is the difference between Senior Molecular Modeling vs Molecular Dynamics Specialist?

AspectSenior Molecular ModelingMolecular Dynamics Specialist
Required CredentialsBachelor's/Master's in Chemistry, Biochemistry, or related fields; experience with modeling softwareBachelor's/Master's in Chemistry, Physics, or related fields; strong background in simulation techniques
Work EnvironmentResearch labs, pharmaceutical companies, biotech firmsResearch labs, pharmaceutical companies, biotech firms
Industry UsageDesigning molecular structures, drug discovery, material scienceRunning molecular dynamics simulations, analyzing simulation data
Common Search/ComparisonOften compared due to overlapping skills in modeling software and research goalsSpecializes in dynamic simulations, but overlaps with modeling tasks

While both roles involve computational chemistry and software tools, Senior Molecular Modeling focuses on creating and analyzing molecular structures, whereas Molecular Dynamics Specialists primarily run and interpret dynamic simulations to understand molecular behavior over time.

What are the key skills and qualifications needed to thrive as a Senior Molecular Modeler, and why are they important?

To thrive as a Senior Molecular Modeler, you need advanced knowledge in computational chemistry, molecular modeling, and structural biology, typically supported by a PhD in a related field. Proficiency with software tools like Schrödinger, MOE, AMBER, and programming languages such as Python or R is essential. Strong problem-solving, communication, and collaborative skills help you effectively interpret results and work within multidisciplinary teams. These skills and qualities are crucial for driving innovative drug discovery and accurately predicting molecular interactions.
What cities are hiring for Senior Molecular Modeling jobs? Cities with the most Senior Molecular Modeling job openings:
What are the most commonly searched types of Molecular Modeling jobs? The most popular types of Molecular Modeling jobs are:
What states have the most Senior Molecular Modeling jobs? States with the most job openings for Senior Molecular Modeling jobs include:
Senior Molecular Modeling jobs near you
Scientific Director, Computational Chemistry

Scientific Director, Computational Chemistry

Neurocrine Biosciences, Inc.

San Diego, CA • On-site

Full-time

Medical, Dental, Vision, Retirement, PTO

Posted 4 days ago

Job description

Who We Are:
Neurocrine Biosciences is a leading biopharmaceutical company with a simple purpose: to relieve suffering for people with great needs. We are dedicated to discovering, developing and commercializing life-changing treatments for patients with under-addressed neurological, psychiatric, endocrine and immunological disorders. The company's diverse portfolio includes FDA-approved treatments for tardive dyskinesia, chorea associated with Huntington's disease, classic congenital adrenal hyperplasia, hyperphagia in patients with Prader-Willi syndrome, endometriosis* and uterine fibroids*, as well as a robust pipeline including multiple compounds in mid- to late-phase clinical development across our core therapeutic areas. For more than three decades, we have applied our unique insight into neuroscience and the interconnections between brain and body systems to treat complex conditions. We relentlessly pursue medicines to ease the burden of debilitating diseases and disorders, because you deserve brave science. For more information, visit neurocrine.com, and follow the company on LinkedIn, X, Facebook and YouTube. (*in collaboration with AbbVie)
About the Role:
Develops and leads innovative computational strategies that accelerate drug discovery across a Research and Development portfolio from early discovery through clinical candidate nomination. Integrates computational approaches including molecular modeling, cheminformatics, molecular dynamics, free energy perturbation, and AI/ML-driven drug design to support data-driven decision-making and the optimization of therapeutics across multiple modalities, including small molecules and biologics. Working within multidisciplinary teams of medicinal chemists, structural biologists, pharmacologists, data scientists, and ADME/Tox representatives, provides molecular-level insight and computational expertise to inform compound design, potency and selectivity optimization, and de-risk design hypotheses. Represents Computational Chemistry across Research and Development functions and seamlessly integrates internal and external technologies, collaborations, and resources to advance Neurocrine's drug discovery strategy. Supports senior leadership through long-term strategic planning, technology innovation, resource management, and the continuous evolution of computational capabilities to ensure effective achievement of scientific and operational objectives. Serves as a mentor and scientific leader, fostering the development of junior scientists and promoting excellence within the computational chemistry function.
Your Contributions (include, but are not limited to):
  • Develops, implements, and enforces scientifically sound computational chemistry strategies that support drug discovery programs from target validation through lead optimization and candidate selection
  • Leads the application of molecular modeling, structure-based drug design, ligand-based design, and AI/ML approaches to enable compound design and optimization
  • Partners closely with medicinal chemistry, structural biology, pharmacology, and data science teams to integrate computational insights into project strategies and decision-making
  • Evaluates, interprets, and communicates computational results, proactively providing strategic direction to project teams and senior management on compound design and program progression
  • Drives innovation through the evaluation and implementation of emerging computational technologies, including generative chemistry, predictive modeling, and large-scale data analysis
  • Establishes and oversees computational workflows, best practices, and reproducible methods to support high-quality and efficient research
  • Represents Computational Chemistry across R&D teams and contributes to program strategy, portfolio discussions, and governance forums
  • Provides strategic oversight for external collaborations, including academic partnerships, technology vendors, and contract research organizations (CROs)
  • Contributes to intellectual property strategy, scientific publications, and external presentations
  • Participates in selecting, developing, and evaluating personnel to ensure efficient operation and growth of the team
  • Maintains current knowledge of industry trends, emerging technologies, and scientific advancements in computational chemistry and drug discovery
  • Other tasks as assigned

Requirements:
  • Bachelors in chemistry or related field AND 12+ years of experience applying computational chemistry in a drug discovery setting OR
  • Masters in computational chemistry or related field AND 10+ years of experience applying computational chemistry in a drug discovery setting OR
  • PhD in computational chemistry, organic chemistry or a related field AND 8+ years of experience applying computational chemistry in a drug discovery setting
  • Proven leadership experience, including managing and developing scientific teams
  • Applies understanding of the team's place in the larger organization, and discusses changes, progress, and issues as they relate to other areas
  • Ability to meet multiple deadlines across a variety of projects/programs, with a high degree of accuracy and efficiency.
  • Deep expertise in molecular modeling, structure-based drug design, and cheminformatics methods
  • Demonstrated experience applying computational approaches to small molecules and/or emerging modalities
  • Experience integrating computational chemistry into multidisciplinary drug discovery teams
  • Strong track record of scientific achievement, including publications and/or patents
  • Experience with AI/ML approaches in drug discovery, including predictive modeling and generative design
  • Deep expertise in ligand and structure-based drug design related to small molecules as well as other modalities including: peptides, biologics and targeted protein degradation
  • Familiarity with CNS drug discovery or neuroscience-focused research
  • Experience working with cloud computing and high-performance computing environments including programming computational workflows in Knime or equivalent.
  • Expertise with industry-standard computational chemistry platforms (e.g., Schrödinger, OpenEye, MOE, or similar)
  • Demonstrated ability to influence strategy across multiple functions and organizational levels
  • Demonstrates strategy development and implementation within areas of responsibility
  • Possesses expert knowledge of own function and broad knowledge of multiple functions and impact on business
  • Proven leadership skills, including influencing across many levels of the organization
  • Maintains broad knowledge of scientific principles and theories and possesses intellectual mastery of multiple scientific areas

#LI-DM1
Neurocrine Biosciences is an EEO/Disability/Vets employer.
We are committed to building a workplace of belonging, respect, and empowerment, and we recognize there are a variety of ways to meet our requirements. We are looking for the best candidate for the job and encourage you to apply even if your experience or qualifications don't line up to exactly what we have outlined in the job description.
The annual base salary we reasonably expect to pay is $218,200.00-$298,000.00. Individual pay decisions depend on various factors, such as primary work location, complexity and responsibility of role, job duties/requirements, and relevant experience and skills. In addition, this position offers an annual bonus with a target of 35% of the earned base salary and eligibility to participate in our equity based long term incentive program. Benefits offered include a retirement savings plan (with company match), paid vacation, holiday and personal days, paid caregiver/parental and medical leave, and health benefits to include medical, prescription drug, dental and vision coverage in accordance with the terms and conditions of the applicable plans.

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