Senior Scientist, Computational Chemistry at Neomorph, Inc. San Diego, CA

Senior Scientist, Computational Chemistry – Neomorph, Inc. – San Diego, CA

Neomorph is looking for a curious, creative, and driven Senior Scientist to join our growing Computational Chemistry team. This is a unique opportunity to work at the forefront of small molecule drug discovery and targeted protein degradation in a fast-paced, collaborative startup environment.

In this role, you’ll actively contribute to every stage of the discovery process — from target selection to advancing chemical series from hits to leads, optimizing leads, and selecting drug candidates. You’ll apply both structure- and ligand-based design approaches to drive innovation across programs and play a key role in evolving Neomorph’s computational chemistry platform.

This individual will have the opportunity to work at a company with a robust biophysics platform that is fully committed to leveraging computational chemistry to advance drug discovery projects from target identification to lead optimization and beyond. With access to cutting-edge CADD software and hardware, the Senior Scientist will make a direct and meaningful impact on the drug discovery process, ultimately improving patient outcomes.

• Work as a key member of the multidisciplinary team of medicinal chemistry, structure biology, biochemistry, and biology and guide the team by providing computational expertise in structure-based drug design and other methods.
• Building and applying suitable hypotheses to design compounds aimed at improving potency, target selectivity, physicochemical and/or pharmacokinetic properties, as evidenced by project impact
• Develop, optimize and deploy novel computational methods and workflows to improve productivity
• Apply molecular dynamics to simulate protein flexibility to allow high-accuracy prediction of binding site, binding mode, and binding kinetics of small molecules.
• Design compounds and predict their potency and ADMET using cutting-edge computational chemistry methods, including physics/ML based activity prediction.
• Drive structure/ligand virtual screening and generative AI methodologies for effective hit identification and hit-to-lead.
• Investigate, explore, and implement state-of-the-art computational chemistry methods that potentially accelerate discovery of molecular glue.

• PhD in Computational Chemistry, or related field with 5+ years, MS with 8+ years or BS with 11+ years of relevant experience
• At least 5 years of experience working as a computational chemist in the pharmaceutical/biotech industry (will consider relevant post‑doctoral work).
• Expertise in structure‑based design, and ligand‑based design with a solid background in physical chemistry, and knowledge of medicinal chemistry principles
• Proven track record of drug design with significant impact on drug discovery projects.
• Team oriented and highly collaborative with a hands‑on approach; take ownership of projects and advance them with a strong sense of urgency in a fast‑paced environment
• Strong interpersonal, communication, influencing and problem‑solving skills and presentation skills at all levels both internally and externally
• Experience in physics‑based activity prediction methods, including MM‑GB/PBSA, FEP, and TI.
• Familiarity with commercial computational chemistry suites. The Schrodinger and Open Eye suites are preferred.
• Proficiency in scientific programming skills (e.g. Python, R) is essential.

• Knowledge and experience of Cloud Computing is plus.
• Expertise in protein‑protein docking tools is plus.
• Knowledge and experience working with Protein‑Protein Interaction targets
• Familiarity with quantum mechanics, cheminformatics, bioinformatics
• Experience in application of MD packages (AMBER, GROMACS, OPENMM) to analyze protein‑ligand or protein‑protein interaction and to estimate ligand affinity is preferred.

• 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…