Pharma Computational Chemist - Onsite, Relocation Available

Cogent Scientific; San Diego (CA); On-site; USD 150,000 - 210,000; Full time

Job summary

Cogent Scientific is seeking a highly skilled Pharma Computational Chemist to lead analysis of protein structures for small-molecule discovery. You will integrate X-ray, cryo-EM, and predicted structures with biophysical data, using Schrödinger and other platforms to guide docking, screening, MD, and free-energy calculations.

The role emphasizes developing testable binding hypotheses, collaborating with medicinal chemists, and advancing AI-enabled design workflows in a fast-paced setting.

Qualifications

• PhD in a computational chemistry/biophysics/structural biology or related field, or equivalent experience.
• Experience using 3D protein structures for drug-discovery questions.
• Experience with docking, virtual screening, MD, or free-energy calculations.
• Ability to write Python scripts in a Linux/HPC environment.

Responsibilities

• Analyze protein structures and complexes to identify binding sites and allosteric opportunities.
• Integrate crystallography, cryo-EM, predicted structures, and biophysical data to guide discovery.
• Apply Schrödinger and other modeling tools to support docking, virtual screening, MD, and free-energy methods.
• Develop binding hypotheses and prioritize compounds for biochemical and cellular evaluation.
• Collaborate with medicinal chemists on binding modes, SAR, and developability.
• Incorporate AI-enabled virtual screening and property prediction into workflows.
• Coordinate with experimental teams to validate predicted mechanisms and binding sites.
• Build reproducible computational workflows with documentation of models and methods.

Skills

Python scripting

Linux HPC

Problem solving

Learning agility

Education

PhD in computational chemistry or related field

Tools

Schrödinger

Molecular modeling platforms

Linux/HPC environments

Job description

Cogent Scientific is seeking a highly skilled Pharma Computational Chemist to lead analysis of protein structures for small-molecule discovery. You will integrate X-ray, cryo-EM, and predicted structures with biophysical data, using Schrödinger and other platforms to guide docking, screening, MD, and free-energy calculations.

The role emphasizes developing testable binding hypotheses, collaborating with medicinal chemists, and advancing AI-enabled design workflows in a fast-paced setting.