HuiLiuCode / CaFE_PluginLinks
a VMD plugin for binding affinity prediction using end-point free energy methods
☆28Updated 9 years ago
Alternatives and similar repositories for CaFE_Plugin
Users that are interested in CaFE_Plugin are comparing it to the libraries listed below
Sorting:
- Computational Chemistry Workflows☆56Updated 3 years ago
- ☆25Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46Updated 4 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Updated 2 years ago
- 3D ligand-based pharmacophore modeling☆53Updated 3 weeks ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆27Updated 3 months ago
- ☆29Updated 9 months ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 11 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆60Updated last month
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Tool suite for analysing molecular dynamics trajectories using network analysis and PRS☆53Updated 8 months ago
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- PyRod - Tracing water molecules in molecular dynamics simulations☆55Updated 3 months ago
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆23Updated last month
- Tool to predict water molecules placement and energy in ligand binding sites☆35Updated 4 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Updated 4 years ago
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆31Updated 8 months ago
- Fully automated high-throughput MD pipeline☆88Updated last week
- A collections of scripts for working molecular dynamics simulations☆45Updated 6 months ago
- MD pharmacophores and virtual screening☆34Updated 2 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated last week
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated 2 years ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆45Updated 4 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- Open-source online virtual screening tools for large databases☆35Updated last month
- An open library to work with pharmacophores.☆49Updated 2 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆40Updated 2 years ago
- ☆69Updated 2 years ago