Senior Computational Chemist: Drug Discovery & ML-Driven Design

Otsuka Pharmaceutical Co., Ltd.; Boston (MA); On-site; USD 140,000 - 190,000; Full time

Job summary

Otsuka Pharmaceutical Co., Ltd. seeks a Senior Scientist in Computational Chemistry to lead design and optimization of drug candidates through physics-based and machine learning methods. You will independently design computational strategies influencing hit-to-clinical candidate decisions.

You will collaborate with medicinal chemists, biologists, and structure biologists to address potency, selectivity, and developability while advancing software workflows for rapid analysis across programs.

Qualifications

• PhD in Computational Chemistry, Biophysics, Medicinal Chemistry, or a related field with substantial industry experience (4+ years) and demonstrated independence of research projects in a cross-functional drug discovery environment.
• Level will be determined based on demonstrated independence, technical depth, project ownership, and ability to influence in a cross-functional drug discovery environment.
• Strong experience in structure-based drug design, including molecular modeling, molecular dynamics simulations, free energy calculations, protein-ligand docking, and structure analysis to support lead optimization efforts.
• Demonstrated ability to work collaboratively in cross-functional drug discovery teams and clearly communicate computational results to experimental scientists.

Responsibilities

• Design and execute molecular modeling, docking, and structure analysis to guide chemistry synthesis priorities and support structure-based drug design efforts for therapeutic projects.
• Collaborate closely with medicinal chemists, biologists and structure biologists to design compounds that address potency, selectivity, and developability objectives.
• Apply physics-based methods (molecular dynamics, free energy calculations) alongside machine learning approaches to improve models and accelerate the design-make-test-analyze cycle for lead optimization.
• Contribute to the development of computational workflows and software that enables rapid analysis of compound designs across multiple programs.
• Stay current with advances in computational chemistry and machine learning for drug discovery to continuously improve methodologies and approaches.

Skills

Molecular modeling

Molecular dynamics simulations

Free energy calculations

Protein-ligand docking

Structure analysis

Cross-functional collaboration

Python programming

Machine learning

AWS

Linux

Education

PhD in Computational Chemistry, Biophysics, Medicinal Chemistry, or a related field

Tools

Python

scikit-learn

PyTorch

TensorFlow

AWS

Linux

GROMACS/AMBER

Job description

Otsuka Pharmaceutical Co., Ltd. seeks a Senior Scientist in Computational Chemistry to lead design and optimization of drug candidates through physics-based and machine learning methods. You will independently design computational strategies influencing hit-to-clinical candidate decisions.

You will collaborate with medicinal chemists, biologists, and structure biologists to address potency, selectivity, and developability while advancing software workflows for rapid analysis across programs.