free-energy-calculations
CommunityPerform free-energy calculations for ligand binding in proteins.
Authorpradyumnasagar
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill addresses the challenge of accurately calculating the free energy of ligand binding to proteins, a critical step in drug discovery and optimization.
Core Features & Use Cases
- Free Energy Calculations: Computes relative and absolute binding free energies using methods like FEP+ and OpenFE, with support for OpenMM, GROMACS, and AMBER.
- Method Comparison: Compares results with machine learning alternatives like Boltz-2 affinity.
- Use Case: For a drug discovery project, quickly rank ligand analogs by binding affinity or optimize lead compounds.
Quick Start
Load the free-energy-calculations skill to perform binding free energy calculations for a protein-ligand pair.
Dependency Matrix
Required Modules
openfeopenmmgromacsamberalchemlybpymbarrdkit
Components
scriptsreferencesassets
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: free-energy-calculations Download link: https://github.com/pradyumnasagar/open-research-skills/archive/main.zip#free-energy-calculations Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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