rinikerlab / reeds
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
☆29Updated 7 months ago
Related projects: ⓘ
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 9 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated 11 months ago
- Set up relative free energy calculations using a common scaffold☆18Updated 3 weeks ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆41Updated last month
- ☆25Updated 8 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated 11 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆26Updated 2 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- ☆25Updated 8 months ago
- Machine Learning model for molecular micro-pKa prediction☆29Updated 3 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- ☆15Updated 7 years ago
- ☆25Updated 5 months ago
- The public versio☆30Updated last year
- Python code for generating Boresch restraints from MD simulations☆17Updated 2 years ago
- Different run and analysis scripts as described in the research guides.☆10Updated 2 years ago
- A middleware python tool for computational drug discovery on HPC architectures☆9Updated 7 months ago
- ☆33Updated 6 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆23Updated 2 years ago
- A package to identify matched molecular pairs and use them to predict property changes.☆24Updated 4 months ago
- Computational Chemistry Workflows☆52Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆10Updated 2 years ago
- This is an package contains tools for setting up hybrid-topology FE calculations☆21Updated 2 weeks ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- Advanced toolkit for binding free energy calculations☆30Updated this week
- Bayesian Multistate Bennett Acceptance Ratio Method☆10Updated this week
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆27Updated last week
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆11Updated last month
- ☆41Updated 2 years ago
- ☆31Updated 2 weeks ago