cbc-univie / transformato
Set up relative free energy calculations using a common scaffold
☆21Updated 4 months ago
Alternatives and similar repositories for transformato:
Users that are interested in transformato are comparing it to the libraries listed below
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆30Updated 11 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- ☆26Updated last month
- ☆25Updated last year
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated last month
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated 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.☆45Updated 2 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- ☆15Updated 8 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆62Updated last year
- Different run and analysis scripts as described in the research guides.☆12Updated 2 years ago
- ☆42Updated 2 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated 2 weeks ago
- Advanced toolkit for binding free energy calculations☆32Updated 2 weeks ago
- This package contains tools for setting up hybrid-topology FE calculations☆25Updated last week
- ☆54Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- A tutorials suite for BioSimSpace.☆20Updated last month
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆28Updated 4 years ago
- Machine Learning model for molecular micro-pKa prediction☆38Updated 3 months ago
- ☆26Updated last year
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆43Updated 3 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆74Updated 7 months ago
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆34Updated 5 months ago
- The public versio☆40Updated last year
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆14Updated last year