seekrcentral / seekr2Links
Simulation-Enabled Estimation of Kinetic Rates - Version 2
☆33Updated 2 weeks ago
Alternatives and similar repositories for seekr2
Users that are interested in seekr2 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.☆34Updated 2 years ago
- ☆25Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆34Updated 3 months ago
- A tutorials suite for BioSimSpace.☆31Updated 2 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆58Updated last week
- ☆28Updated 7 months ago
- Computational Chemistry Workflows☆56Updated 3 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 4 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆17Updated last year
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46Updated 4 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 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.☆21Updated 7 months ago
- Free Parametrization for Small Molecules☆49Updated 2 months ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated 2 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 4 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆28Updated 2 months ago
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆55Updated 2 weeks ago
- Fully automated high-throughput MD pipeline☆86Updated this week
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 6 months ago
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Updated last year
- ☆44Updated 3 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- ☆38Updated 4 months ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆28Updated 2 weeks ago
- moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ☆39Updated last month
- ☆34Updated last year
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆42Updated last month