How-To Guide and Tutorials

These tutorials discuss the use of specific floes and how to evaluate the results.

MD Affinity Floes

• FE-NES Tutorial
  • FE-NES for Binding Affinity Prediction Floe
  • How to Use the Floe
    • Lauching the FE-NES for Binding Affinity Prediction Floe
    • Minimal Inputs for a New FE-NES Calculation
  • Outputs from FE-NES
  • Additional Inputs for FE-NES
    • Edge Map Type
    • Hub Selection for Star Map Edge Types
    • Running Rapid FE-NES
    • Reusing Existing End-State Simulations
    • Custom Edge Map
    • Providing Experimental Affinities for Ligands
    • Protein Settings and Ligand Settings
    • Solution Environment Settings
    • End-State Simulation Settings
    • Alchemical Switching Settings
    • Output File Names
    • Advanced Compute Resources Settings
    • Job Guardrails
  • Under the Hood
  • Additional Resources
• Rapid FE-NES
  • How to Run Rapid FE-NES on Orion
    • Floe Inputs
    • Locate and Launch the Floe
    • Define Floe Inputs and Submit the Job
    • Monitoring Progress
    • Analyzing Outputs
  • Getting Help with Rapid FE-NES
• Short Trajectory MD with Analysis
  • How-To Guide and Tutorials
    • How-To Guide for the Short Trajectory MD with Analysis Floe
    • Short Trajectory MD with Analysis for Pose Validation
    • Short Trajectory MD with Analysis for FE-NES
• Edge Mapper for RBFE Calculations
  • The Floe Inputs
  • How to Use the Floe
  • How to Edit the Mapper Edges
• Extend MD Simulations
  • Floe Input and Outputs
  • How to Use the Floe
• Bespoke and Custom Force Field
  • Example Case: Biphenyl and Ring Substituents
  • Floe Inputs
  • How to Apply the Bespoke Force Field
  • How to Apply a Custom Force Field
• Using the Recovery Dataset for MD Floes

Induced-Fit Posing (Confined) Floe

• Induced-Fit Posing (Confined)
  • How-To Guide
  • Tutorial