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Entry Level Computational Chemistry Molecular Modeling Jobs

1910

Computational Theoretical Chemist I

Boston, MA

... chemistry insights to aid in the development of AI/ML models for drug discovery as well as the ... Proficiency in analyzing molecular properties such as solvation free energy, dipole moments ...

1910

Computational Theoretical Chemist I

Boston, MA · On-site

... molecule therapeutics discovery by integrating massive multimodal data, frontier AI models, and ... Own computational theoretical chemistry programs across therapeutic modalities, disease targets ...

1910

Computational Theoretical Chemist I

Boston, MA

... molecule therapeutics discovery by integrating massive multimodal data, frontier AI models, and ... Own computational theoretical chemistry programs across therapeutic modalities, disease targets ...

1910

Computational Theoretical Chemist II

Boston, MA · On-site

... molecule therapeutics discovery by integrating massive multimodal data, frontier AI models, and ... Own computational chemistry programs across therapeutic modalities, disease targets, and ...

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How much do entry level computational chemistry molecular modeling jobs pay per year?

As of Aug 8, 2026, the average yearly pay for entry level computational chemistry molecular modeling in the United States is $48,298.00, according to ZipRecruiter salary data. Most workers in this role earn between $38,000.00 and $55,500.00 per year, depending on experience, location, and employer.

What is an entry level computational chemistry molecular modeling?

An entry level computational chemistry molecular modeling job involves using computer simulations and mathematical models to study the structure, properties, and interactions of molecules. Professionals in this role typically work with specialized software to analyze chemical data, predict molecular behavior, and assist in drug discovery or materials science projects. Entry-level positions often require a background in chemistry, physics, or a related field, as well as some experience with programming or computational tools. These roles are commonly found in academic, pharmaceutical, and technology research settings.

What are the key skills and qualifications needed to thrive as an entry level computational chemistry molecular modeling professional?

To thrive as an Entry Level Computational Chemistry Molecular Modeling professional, you need a solid background in chemistry, physics, and mathematics, typically supported by a bachelor's or master's degree in chemistry or a related field. Familiarity with molecular modeling software (such as Gaussian, Schrödinger, or AMBER) and basic programming skills in Python or similar languages are highly beneficial. Strong analytical thinking, attention to detail, and the ability to communicate complex results clearly are valuable soft skills in this role. These skills and qualifications are crucial for accurately modeling molecular systems, interpreting data, and collaborating effectively with interdisciplinary research teams.

What are some common challenges faced by entry level computational chemistry molecular modeling professionals, and how can they overcome them?

Entry-level professionals in computational chemistry molecular modeling often face challenges such as learning to use complex simulation software, interpreting large datasets, and understanding the nuances of molecular interactions. Adapting to the interdisciplinary nature of the field can also be demanding, as it frequently requires collaboration with chemists, biologists, and data scientists. To overcome these challenges, new hires should actively seek mentorship, participate in training workshops, and regularly communicate with their team to clarify project goals and expectations. This proactive approach can accelerate skill development and build confidence in contributing to research projects.
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Entry Level Computational Chemistry Molecular Modeling jobs near you
Infographic showing various Entry Level Computational Chemistry Molecular Modeling job openings in the United States as of August 2026, with employment types broken down into 74% Full Time, 13% Part Time, and 13% Contract. Highlights an 100% In-person job distribution, with an average salary of $48,298 per year, or $23.2 per hour.

Scientist II/Senior Scientist, Computational Chemistry, Drug Discovery

Lila Sciences

Cambridge, MA • On-site

Full-time

Medical, Dental, Vision, Life

Posted 5 days ago

Job description

Your Impact at LILA
Lila Sciences is seeking a Scientist, Computational Chemistry, Drug Discovery to help guide, evaluate, and improve AI-driven drug discovery workflows. This person will bring practical computational chemistry experience in a drug discovery context and will work alongside AI systems to make sure agent-generated optimization plans, compound prioritizations, and modeling workflows are chemically and scientifically sensible. The primary mandate is to make agent-guided discovery scientifically useful, while also contributing directly to live drug discovery programs when human computational chemistry leadership is needed.
This is a role for someone who can look at an agent-driven drug optimization rollout and answer hard questions: Does this plan make sense? Are the right compounds being prioritized? Are the right modeling tools being used? What additional tools, constraints, or review steps should be built so agents can make better discovery decisions? When needed, this person can also step into an active discovery effort and lead the computational chemistry strategy for pursuing a drug program. The role spans docking, virtual screening, SAR modeling, molecular property prediction, compound prioritization, medicinal chemistry support, live program support, and, most centrally, the design and supervision of computational chemistry tools for agentic workflows.
What You'll Be Building
  • Monitor and review drug discovery agents' computational chemistry workflows, recommendations, and optimization plans for scientific and chemical validity.
  • Evaluate agent-generated drug discovery plans that combine chemistry, biophysics, cofolding, simulation, assay, and low-data model outputs, and determine whether the resulting optimization strategy is scientifically coherent.
  • Advise on compound prioritization across discovery programs, including tradeoffs between potency, selectivity, developability, uncertainty, and experimental feasibility.
  • Define which computational chemistry tools agents should use, when they should use them, what inputs are required, and how outputs should be interpreted.
  • Lead computational chemistry strategy for live drug discovery programs when needed, including hypothesis generation, modeling plans, compound prioritization, and interpretation of results.
  • Build, adapt, or guide the creation of open-source-first workflows for docking, virtual screening, SAR analysis, conformer generation, pharmacophore modeling, QSAR, ADMET and property modeling, and cheminformatics.
  • Apply protein-ligand binding modeling to support hypothesis generation, compound design, and prioritization.
  • Partner with medicinal chemists, biologists, computational biophysicists, cofolding and low-data ML scientists, and research engineers to improve AI-assisted discovery loops.
  • Evaluate agent-generated molecular design ideas and identify when proposed chemistry, binding hypotheses, or optimization strategies are weak or unsupported.
  • Help establish validation standards, review protocols, and guardrails for computational chemistry tools used by AI systems.
  • Translate computational chemistry judgment into practical requirements for agent tools, workflows, benchmarks, and decision criteria.

What You'll Need to Succeed
  • PhD or equivalent experience in computational chemistry, chemistry, cheminformatics, molecular modeling, biophysics, or a related field.
  • Strong practical experience applying computational chemistry in a drug discovery context, including active program support or leadership.
  • Demonstrated history of modeling protein-ligand binding and using those models to inform discovery decisions.
  • Working knowledge across docking, virtual screening, SAR modeling, conformer generation, pharmacophore modeling, QSAR, ADMET or property prediction, and cheminformatics.
  • Strong medicinal chemistry experience and the ability to reason about compound optimization, SAR, developability, and synthetic or experimental tradeoffs.
  • Fluency in Python and hands-on experience building open-source computational chemistry workflows with libraries such as RDKit, Biopython, OpenMM, MDAnalysis, or comparable tools.
  • Ability to evaluate computational recommendations critically and communicate uncertainty, assumptions, and limitations clearly.
  • Comfort working alongside AI systems, including reviewing, guiding, and improving agent-generated plans rather than only executing human-authored workflows.
  • Strong collaboration skills across chemistry, biology, ML, computational science, and engineering teams.

Bonus Points For
  • Industry drug discovery experience, especially in computational chemistry, structure-based discovery, or medicinal chemistry project support.
  • Experience extending, integrating, or contributing to open-source scientific software.
  • Experience with FEP, MM/GBSA, molecular dynamics, or other physics-based scoring workflows.
  • Experience integrating computational chemistry workflows into automated or agentic systems.
  • Exposure to DEL, high-throughput screening, or other large experimental datasets.
  • Experience with prospective compound prioritization in active discovery programs.

Compensation
We offer competitive base compensation with bonus potential and generous early-stage equity. Your final offer will reflect your background, expertise, and expected impact.
U.S. Benefits. Full-time U.S. employees receive a comprehensive benefits program including medical, dental, and vision coverage; employer-paid life and disability insurance; flexible time off with generous company wide holidays; paid parental leave; an educational assistance program; commuter benefits, including bike share memberships for office based employees; and a company subsidized lunch program.
International Benefits. Full-time employees outside the U.S. receive a comprehensive benefits program tailored to their region. USD salary ranges apply only to U.S.-based positions; international salaries are set to local market.
Expected Base Salary Range
$140,800-$217,800 USD
About LILA
Lila Sciences is building Scientific Superintelligence™ to solve humankind's greatest challenges. We believe science is the most inspiring frontier for AI. Rather than hard-coding expert knowledge into tools, LILA builds systems that can learn for themselves.
LILA combines advanced AI models with proprietary AI Science Factory™ instruments into an operating system for science that executes the entire scientific method autonomously, accelerating discovery at unprecedented speed, scale, and impact across medicine, materials, and energy. Learn more at www.lila.ai.
Guided by our core values of truth, trust, curiosity, grit, and velocity, we move with startup speed while tackling problems of historic importance. If this sounds like an environment you'd love to work in, even if you don't meet every qualification listed above, we encourage you to apply.
We're All In
Lila Sciences is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.
Information you provide during your application process will be handled in accordance with our Candidate Privacy Policy.
A Note to Agencies
Lila Sciences does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Lila Sciences or its employees is strictly prohibited unless contacted directly by Lila Science's internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Lila Sciences, and Lila Sciences will not owe any referral or other fees with respect thereto.

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