Associate Principal / Principal Scientist, Computational Chemistry

Neomorph•San Diego, CA

57d•$176,000 - $240,000

About The Position

Neomorph is seeking a highly experienced and strategically minded Associate Principal Scientist or Principal Scientist in Computational Chemistry to join our dynamic and collaborative discovery team. This is a hands-on, individual contributor role - you will lead cutting-edge computational chemistry efforts, roll up your sleeves to generate design hypotheses and deliver actionable insights, while influencing program strategy and scientific direction. Whether you join as an Associate Principal or Principal level depends on your years of experience and track record. In either case, you will play a key role in advancing our discovery pipeline from target assessment through candidate nomination, partnering with medicinal chemistry, structural biology, biophysics, and biology teams.

Requirements

Associate Principal Scientist level: 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.
Principal Scientist level: Ph.D. in Computational Chemistry, Theoretical Chemistry, Chemistry or related field with 8+ years, M.S. with 11+ years or B.S. with 14+ years of relevant industry experience.
For both levels: Demonstrated hands-on experience in small-molecule drug discovery, with proven ability to apply molecular modeling, docking, free energy calculations, QSAR/ML, and cheminformatics to support compound design and progression.
Strong record of working independently and delivering high-quality scientific work, while also collaborating effectively in cross-functional teams.
Proficiency with commercial and/or open source computational chemistry and molecular modeling software (e.g., Schrödinger, OpenEye, AMBER, GROMACS, etc.), and fluency in scripting/programming (e.g., Python, R).
Excellent communication and collaboration skills, with ability to influence project teams and senior leadership through scientific insight.
Self-starter attitude, willing to roll up sleeves and execute hands-on work while contributing strategically.
Please note: This role is not a people-manager/line-management position - it is a senior individual contributor role, intended for a strong computational scientist who thrives doing the work directly and influencing through scientific leadership rather than managerial oversight.

Responsibilities

Serve as the primary computational chemistry contributor on one or more drug discovery programs - designing, executing and interpreting computational workflows to support hit identification, hit-to-lead, and lead optimization.
Integrate structure- and ligand-based design, cheminformatics, predictive modeling and molecular simulation to propose novel compounds and drive progression of small-molecule therapeutics (including molecular glues/degraders).
Translate SAR, structural and modeling data into innovative design hypotheses; prioritize compounds and support decision-making alongside drug discovery teams.
Collaborate cross-functionally with medicinal chemistry, structural biology, biophysics, and biology to impact program strategy, compound design and project milestones.
Develop, optimize and deploy computational tools, workflows and methods (e.g., docking, MD, free energy calculations, ML/AI-driven design) to enhance our internal capabilities and accelerate discovery.
Present scientific results and strategic recommendations to internal project teams and senior leadership; provide mentorship and scientific guidance to less-experienced colleagues (without direct line-management responsibility).
Stay abreast of emerging computational chemistry technologies, apply deep domain knowledge and help shape the future of our computational capability.

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)
We believe in work/life balance and Fun is at the core of our Core Values. In addition to department and company happy hours, we have regular company-wide and department lunches and social events (ie Padres games, summer picnic, holiday party, bring your kids to work day).