durrantlab / POVMELinks
Detect and characterize binding pockets from molecular simulations.
☆14Updated 7 months ago
Alternatives and similar repositories for POVME
Users that are interested in POVME are comparing it to the libraries listed below
Sorting:
- Fully automated high-throughput MD pipeline☆88Updated last week
- Random Acceleration Molecular Dynamics in GROMACS☆43Updated 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.☆60Updated last month
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated last week
- ☆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
- A collections of scripts for working molecular dynamics simulations☆45Updated 6 months ago
- ☆70Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆35Updated 4 months ago
- ☆34Updated last year
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Updated last month
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46Updated 4 years ago
- 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
- Computational Chemistry Workflows☆56Updated 3 years ago
- An open library to work with pharmacophores.☆49Updated 2 years ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆22Updated 8 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆40Updated 2 years ago
- Simple protein-ligand complex simulation with OpenMM☆91Updated 2 years ago
- This package contains tools for setting up hybrid-topology FE calculations☆35Updated 3 weeks ago
- ☆69Updated 2 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆91Updated 6 months ago
- Different run and analysis scripts as described in the research guides.☆13Updated 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
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Force Fields☆67Updated last year
- A python module to plot secondary structure schemes☆25Updated 2 years ago
- ☆29Updated 9 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 6 years ago
- Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium☆46Updated last month