Scientist / Senior Scientist, Structure-Based Modeling

Deep Origin; Portugal; Remote; EUR 50,000 - 75,000; Full time

Benefits offered by this job

Competitive salary and equity packages

Flexible working hours

Mission-driven culture

Job summary

A leading biotech company in Portugal is looking for a Scientist or Senior Scientist with expertise in structure-based drug design. The role involves designing simulations, analyzing protein-ligand structures, and collaborating with various teams. Candidates must have a Ph.D. and relevant experience in molecular dynamics and docking. This position offers competitive salary and a flexible, remote-first work environment.

Qualifications

• 2+ years of postdoctoral or industry experience in structure-based modeling.
• Hands-on expertise with free energy perturbation (FEP).
• Strong understanding of protein-ligand binding and conformational variability.

Responsibilities

• Analyze protein targets focusing on conformations and binding site flexibility.
• Run and refine docking and molecular dynamics simulations.
• Collaborate with cheminformatics and experimental teams.

Skills

Expertise in structure-based drug design

Molecular dynamics simulation

Docking

Programming in Python

Fluency in English

Education

Ph.D. in computational chemistry or related field

Tools

GROMACS

OpenMM

Schrödinger FEP+

Job description

Scientist / Senior Scientist, Structure-Based Modeling

Scientist / Senior Scientist, Structure-Based Modeling

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Deep Origin is seeking a Scientist or Senior Scientist with strong expertise in structure-based drug design, including docking, molecular dynamics (MD), and free energy perturbation (FEP), to support a transformative ARPA-H initiative. You'll lead the design of robust simulation workflows and analyze protein-ligand structures across a large target panel to support predictive modeling for therapeutic discovery.

Requirements

• Ph.D. in computational chemistry, structural biology, biophysics, or related field;
• 2+ years of postdoctoral or industry experience in structure-based modeling;
• Hands-on expertise with FEP (RBFE/ABFE), including best practices around setup, sampling, and analysis;
• Proficiency with one or more simulation platforms (e.g., Schrödinger FEP+, OpenMM, GROMACS, AMBER, NAMD);
• Strong understanding of protein-ligand binding, structure selection, and conformational variability;
• Programming experience in Python, and familiarity with tools like MDAnalysis, PyMOL APIs, or MDTraj;
• Fluent English for collaboration with an international team;
• Ability to work on US time zones when needed
  
  

Nice to have:

• Experience benchmarking across multiple PDB entries or conformational states;
• Prior work integrating structural modeling into machine learning pipelines;
• Familiarity with MM/GBSA, docking scoring functions, or clustering methods;
• Experience using Unix-based HPC environments, workload managers (e.g., SLURM, etc.), and optionally AWS;
• Comfort managing large-scale simulation data for modeling or analysis
  
  

Responsibilities:

• Analyze tens to hundreds of protein targets relevant to ADMET and off-targets, focusing on conformations, binding site flexibility, and ligand-bound states to guide structure preparation and ensemble design;
• Run and refine docking, MD, and FEP (RBFE and ABFE) simulations using state-of-the-art tools;
• Apply methods such as restraints, alchemical transformations, and sampling strategies to ensure robust and reproducible FEP workflows;
• Curate, benchmark, and select optimal protein-ligand structures (e.g., from PDB) for predictive modeling;
• Evaluate multiple structural representations (e.g., different PDB IDs) to determine the best input per target;
• Collaborate with cheminformatics, ML, and experimental teams to integrate structure-based insights across discovery pipelines;
• Communicate progress, technical findings, and challenges across internal and external teams
  
  

Why Join Deep Origin

Deep Origin builds modern infrastructure for computational science at the interface of biology, chemistry, and AI. As part of our ARPA-H program, you'll shape the future of structure-based modeling for therapeutics.

We offer:

• A remote-first team across the US, Europe, and Armenia;
• Competitive salary and equity packages;
• Flexible working hours;
• A mission-driven, scientifically rigorous culture that values autonomy and impact

Seniority level

• Seniority level

  Mid-Senior level

Employment type

• Employment type

  Full-time

Job function

• Job function

  Other

• Industries

  IT Services and IT Consulting

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