rinikerlab / reedsLinks
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.
☆31Updated last month
Alternatives and similar repositories for reeds
Users that are interested in reeds are comparing it to the libraries listed below
Sorting:
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- A tutorials suite for BioSimSpace.☆25Updated 2 months ago
- ☆29Updated last month
- ☆25Updated last year
- ☆15Updated 8 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆50Updated 3 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- Set up relative free energy calculations using a common scaffold☆24Updated 2 months ago
- Machine Learning model for molecular micro-pKa prediction☆42Updated 9 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 2 years ago
- A package to identify matched molecular pairs and use them to predict property changes.☆24Updated last year
- This package contains tools for setting up hybrid-topology FE calculations☆29Updated 2 weeks ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Updated 4 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆14Updated 2 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆71Updated 2 years ago
- ☆27Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated last week
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 10 months ago
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- Alchemical mutation scoring map☆39Updated 4 months ago
- ☆28Updated 2 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 4 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆22Updated 10 years ago