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.
☆32Updated 2 months ago
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
- ☆25Updated 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.☆50Updated 4 months ago
- ☆15Updated 8 years ago
- A tutorials suite for BioSimSpace.☆25Updated 3 months ago
- Machine Learning model for molecular micro-pKa prediction☆43Updated 10 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆27Updated 7 months ago
- ☆27Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆29Updated 2 weeks ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 3 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated last year
- ☆34Updated last year
- ☆32Updated last year
- ☆44Updated 3 years ago
- This package contains tools for setting up hybrid-topology FE calculations☆29Updated last month
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated last month
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 11 months ago
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- Dynamic pharmacophore modeling of molecular interactions☆35Updated last year
- ☆28Updated 2 months ago