Associate Principal Scientist, Computational Chemistry

Neomorph • San Diego, CA

187d

About The Position

Neomorph is seeking a highly experienced and strategic Associate Principal Scientist to join our dynamic and collaborative Computational Chemistry team. This individual contributor role is ideal for someone who thrives in a fast-paced startup environment and is eager to shape the future of targeted protein degradation and small molecule drug discovery. As a senior member of the Computational Chemistry group, you will play a critical role in advancing discovery programs from target assessment through candidate nomination. You'll partner closely with medicinal chemistry, structural biology, biophysics, and biology colleagues to integrate computational strategies into program decision-making. Beyond direct project impact, you will also help drive the evolution of Neomorph's computational capabilities, championing innovation and deploying novel tools and methods. This is a unique opportunity to contribute scientifically while helping to shape the strategic direction of a growing function at the cutting edge of degrader drug discovery.

Requirements

• PhD in Computational Chemistry, Theoretical Chemistry, or a related field with 6+ years, MS with 9+ years, or BS with 12+ years of relevant industry experience in drug discovery.
• Demonstrated impact as a lead computational chemist on drug discovery programs, including significant contributions to compound progression and decision-making.
• Deep expertise in structure-based drug design, molecular modeling, and ligand-based approaches, with working knowledge of medicinal chemistry principles.
• Hands-on experience with molecular dynamics simulations (e.g., AMBER, GROMACS, OpenMM) and free energy calculations (e.g., FEP+, TI, MM-GBSA).
• Proficiency in relevant commercial and open-source software suites (e.g., Schrödinger, OpenEye) and fluency in scripting/programming languages (e.g., Python, R).
• Proven ability to integrate complex data and translate computational insights into actionable recommendations.
• Strong communication, collaboration, and problem-solving skills with the ability to influence cross-functional teams and drive strategic discussions.

Nice To Haves

• Experience applying generative AI, machine learning, or advanced cheminformatics techniques to small molecule design.
• Familiarity with targeted protein degradation or protein-protein interaction drug discovery.
• Experience in developing and optimizing cloud-based computational workflows.
• Knowledge of quantum chemistry methods, bioinformatics tools, and/or data integration strategies.

Responsibilities

• Serve as a scientific lead and primary computational chemistry contributor on one or more drug discovery programs, guiding design strategies through all phases of the discovery process.
• Integrate structure- and ligand-based design, cheminformatics, and predictive modeling approaches to accelerate hit identification, hit-to-lead, and lead optimization.
• Design and prioritize novel compounds using hypothesis-driven approaches informed by structural data, SAR, molecular modeling, and ML/AI tools.
• Apply and enhance state-of-the-art computational chemistry methodologies, including protein-ligand docking, molecular dynamics (MD), free energy calculations, and ADMET prediction.
• Collaborate cross-functionally to influence program strategy and compound design, bringing both depth and creativity to design hypotheses.
• Explore and evaluate new computational tools, workflows, and platforms to expand and enhance Neomorph's internal capabilities.
• Mentor and provide scientific guidance to less experienced team members across functions; contribute to project team leadership through influence, not direct line management.
• Present findings and strategic recommendations to cross-functional teams and scientific leadership.

Benefits

• Industry competitive compensation
• Annual target bonus
• Stock options
• 401K plan
• Career advancement opportunities
• Monthly town halls to share business and scientific updates
• Comprehensive medical, dental, and vision plans for employees and their dependents
• Health and Dependent Care FSA and HSA Plan with monthly Neomorph contribution
• Employee Assistance Program
• 10 holidays + Winter Shutdown + 3 weeks of vacation time with additional accruals after 2nd year of employment, separate sick leave.
• Supplemental pay for Pregnancy Disability Leave
• Paid Parental Leave for employees with a newborn child or a child placed with them for adoption or foster care
• Casual work environment
• Volunteer days off each year to spend time contributing to causes you care about
• Flexible work schedule
• Access to onsite gym
• Onsite space to store your bicycle (or surfboard)
• Regular company-wide and department lunches and social events (ie Padres games, summer picnic, holiday party, bring your kids to work day)

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Industry: Chemical Manufacturing
• Education Level: Ph.D. or professional degree
• Number of Employees: 51-100 employees