easybfe-cli

What problem does it solve?

This Skill removes the friction of preparing and analyzing protein-ligand binding free energy workflows, helping you move from raw ligands and a receptor structure to runnable EasyBFE simulation directories and results.

Core Features & Use Cases

• Ligand Parameterization: Prepare Amber-compatible ligand directories for downstream absolute and relative binding free energy workflows.
• ABFE and RBFE Setup: Generate the correct simulation layout, config-driven run directories, and restraint or mapping setup for one ligand or many ligands.
• Result Analysis: Run MBAR-based analysis on completed simulation trees and summarize binding free energy outputs.
• Use Case: A computational chemist can take a protein structure and a ligand set, generate the required EasyBFE inputs, launch the simulation prep workflow, and then analyze the finished ABFE or RBFE runs consistently.

Quick Start

Ask for an EasyBFE workflow that parameterizes my ligands, prepares the ABFE or RBFE configuration from my protein file, and sets up the run directories for analysis.