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Scientist II, Computational Biology/Molecular Dynamics



San Diego, CA, USA
Posted on Tuesday, April 30, 2024

About this position:

Working with leaders in the field of targeted protein degradation, you will be engaged in development of advanced computational and AI/machine learning methods to establish novel methods for Drug Discovery and selection of therapeutic targets. This is a highly collaborative position which will focus on using advanced molecular dynamics simulation techniques to investigate the mechanistic details of protein-protein interactions, as well as applying protein-protein docking and artificial intelligence /machine learning to predict complex structure with high accuracy.


  • Develop and apply computational tools to predict protein-protein interaction potential and to select candidate proteins for study.
  • Develop high accuracy scoring functions of protein-ligand interactions, such as free energy perturbation (FEP), thermodynamic integration (TI), and AI/machine learning methods.
  • Implement an HPC cloud environment for high-throughput computational drug design by docking, molecular dynamics, and free energy approaches.
  • Apply MD or relevant methods to predict ligandable sites.
  • Collaborate with medicinal chemists to translate computational predictions into ligand designs and provide guidance for compound synthesis and screening.
  • Perform virtual screening and molecular modeling studies to identify and prioritize potential protein targets for degradation.
  • Analyze and interpret experimental data, including binding affinities and protein degradation data to guide compound optimization.
  • Develop and maintain computational chemistry and biology tools and workflows to streamline and enhance the efficiency of protein modeling, virtual screening and compound design processes.
  • Stay up-to-date with the latest advancements in molecular dynamics, protein degradation, and drug discovery fields, and proactively apply new techniques and methodologies to improve project outcomes.
  • Contribute to scientific publications, patents, and presentations to communicate research findings and contribute to the intellectual property portfolio of the company.
  • Collaborate effectively within cross-functional teams, providing computational insights and expertise to support project goals and timelines.

Required Qualifications:

  • Ph.D. in Computational Chemistry, Computational Biology, Computational Biophysics or related field with 2+ years, MS with 5+ years or BS with 8+ years of relevant industry experience
  • Strong understanding of molecular dynamics, enhanced sampling methods, free energy approaches, and their application to drug design.
  • Background in the computational prediction of protein-protein interaction.
  • Experience in running molecular dynamics to a protein-ligand complex and analyzing trajectory to explore key elements of the interaction.
  • Experience in molecular dynamics software such as AMBER, GROMACS, and NAMD
  • Robust coding experience using modern scientific languages (Python/C++/etc.).
  • Experience with Python API to analyze protein dynamics and protein-ligand interaction, i.e., (MDTraj, MDAnalysis, and Schrodinger Python API).
  • Mastery of Linux OS and command-lines.
  • Experience in distributed computing using HPC clusters or cloud platforms.
  • Experience with commercial modeling tools, i.e., Schrodinger and OpenEye.

Preferred Qualifications:

  • Ability to communicate, collaborate and deliver results as a member of multi-disciplinary teams.
  • Run virtual screening and prioritize compounds for biological assessment.
  • Basic knowledge of medicinal chemistry.
  • Experience with computational approaches to fragment-based ligand design or DNA encoded libraries.

What we offer:

  • Industry competitive compensation
  • Annual target bonus
  • Stock options
  • 401K plan
  • Company-paid external career development coaching program
  • Career advancement opportunities
  • Monthly town halls to share business and scientific updates

Work Hard, Stay Well

  • 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)

Have Fun!

We believe in work/life balance and Fun is at the core of our Core Values. In addition to 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).

About Us:

Neomorph is a venture backed biotechnology company solving critical problems in human health through the discovery and development of innovative new medicines against ‘undruggable targets’. Our team is comprised of industry leading experts in protein degradation and molecular glues who have a track record of ground-breaking discoveries in the field. We are committed to leadership in advancing the science and technology of molecular glue drug discovery, while prosecuting a pipeline of projects through clinical development. Our patient-first, science-driven approach is complemented by our dedication to a supportive and collaborative work environment.

Neomorph is headquartered in San Diego, California, and has a key collaboration with the Center for Protein Degradation at the Dana-Farber Cancer Institute.

Neomorph is committed to pursuing and hiring a diverse workforce and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of any characteristic protected by applicable federal, state or local law.