Resources¶
GROMACS¶
- GROMACS Documentation
- GROMACS User Guide
- GROMACS Reference Manual
- GROMACS Tutorials
- MD Tutorial
- Biobb Workflows
Schrödinger FEP+¶
Tutorials¶
- BACE1 RBFE Tutorial
- FEP+ Pose Generation
- Protein FEP Thermostability — T4 Lysozyme
- FEP+ Residue Scanning — Lambda Dynamics
- Consensus IFD-MD + FEP+
- Ligand FEP Tutorial — Release 15-3
- Temple University FEP Lab Manual — fXa System
- FEP+ for GPCR — DISI/Shoichet Lab Membrane FEP Workflow
- FEP+ Training Course
Docs and Manual¶
- FEP+ User Manual
- FEP+ Content Library
- FEP+ Free Learning Resources
- FEP+ GPU Performance Data
- FEP+ System Requirements
- FEP+ for Academic Research
- FEP+ CLI Source — All Flags and Usage
- FEP+ Python API
Best Practices¶
- Best Practices for FEP+ Use — Full Official Text on Zhihu
- D3R Webinar Slides — FEP Setup Best Practices by Cournia Lab
Chinese Resources¶
- Academic Schrödinger FEP on Baidu AI Studio
- Schrödinger Tutorial — Drug Development with Macrocycles Including FEP+
- Desmond 2022-4 Chinese Translation Including FEP+ Overview
- Schrödinger Beginner Q&A
- DeepPotential Hermite FEP Tutorial
- Uni-FEP Introduction and FEP Application Scenarios
Key Literature¶
- Wang et al. JACS 2015 — FEP+ Original Validation
- Wang et al. Methods Mol Biol 2019 — FEP+ Methodology and Best Practices
- Comm. Chem. 2023 — Maximal and Current Accuracy of FEP
- Merck Large-Scale Prospective FEP+ Evaluation
OpenFE¶
Tutorials¶
- OpenFE Tutorials Index
- Python API Showcase — RBFE Introduction
- RBFE with the Python API — TYK2 Step-by-Step
- RBFE with the CLI — TYK2 Step-by-Step
- Absolute Binding Free Energy — Toluene to T4 Lysozyme
- Absolute Solvation Free Energy — Benzene Hydration
- SepTop Protocol — Separated Topologies RBFE
- Example Notebooks Repository
Docs and Manual¶
- OpenFE Documentation Home
- OpenFE User Guide
- OpenFE Cookbook
- OpenFE CLI and Python API Reference
- OpenFE Protocol Details
- OpenFE GitHub Repository
- OpenFE Website