HuiLiuCode / CaFE_PluginLinks
a VMD plugin for binding affinity prediction using end-point free energy methods
☆27Updated 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:
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- Computational Chemistry Workflows☆55Updated 3 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆24Updated 2 months ago
- ☆25Updated last year
- ☆28Updated 4 months ago
- Fully automated high-throughput MD pipeline☆70Updated 2 weeks ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆19Updated 4 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated last year
- Fully automated docking pipeline (can be run in distributed environments)☆48Updated last week
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated last month
- PyRod - Tracing water molecules in molecular dynamics simulations☆50Updated 4 years ago
- 3D ligand-based pharmacophore modeling☆50Updated 4 months ago
- Machine Learning Boosted Docking (HASTEN): Accelerate Structure-based Virtual Screening☆39Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆51Updated 5 months ago
- ☆46Updated 4 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 6 months ago
- Tool suite for analysing molecular dynamics trajectories using network analysis and PRS☆50Updated 3 months ago
- Open-source tool for synthons-based library design.☆82Updated 8 months ago
- ☆10Updated 5 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆71Updated 7 months ago
- An open library to work with pharmacophores.☆45Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- MD pharmacophores and virtual screening☆33Updated last year
- ☆17Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last month
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆14Updated 4 years ago