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Research Intern – Computer Aided Drug Design

Alkermes
Waltham, MA Intern
POSTED ON 2/25/2025
AVAILABLE BEFORE 5/22/2025

The Structure-based Modeling group in Alkermes Inc in Waltham MA is seeking an outstanding graduate student to team for a 12-week summer internship program. The position will be responsible for running molecular modeling to test hypotheses, providing data-driven analyses, and developing in-house binding free energy calculation workflows for membrane proteins. The successful candidate will work with senior computational chemists and medicinal chemists to provide molecular modeling support for drug discovery portfolio. This position will be office-based and 100% on-site.

Basic Qualifications / Required skills include, but are not limited to, the following :

  • Must be enrolled in a program with a major in computational chemistry or similar fields.
  • Proficiency in molecular dynamics simulations and binding free energy calculations.
  • Experience using Linux OS, HPC cluster and command line interface.
  • Proficiency in Python.
  • Experience with a modern MD simulation engine (., AMBER, OpenMM).
  • Experience with MD simulation of small molecules.

Preferred Qualifications :

  • Deep understanding of binding free energy calculations in theory and practical set-up.
  • Experience with membrane protein modeling.
  • Experience with open-source python packages development.
  • Experience with structure-based modeling software such as MOE and / or Maestro
  • This position will be office-based and 100% on-site.

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