emleddin / research-scriptsLinks
Different run and analysis scripts as described in the research guides.
☆13Updated 3 years ago
Alternatives and similar repositories for research-scripts
Users that are interested in research-scripts are comparing it to the libraries listed below
Sorting:
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 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.☆60Updated 3 weeks ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆70Updated 2 years ago
- Machine Learning model for molecular micro-pKa prediction☆47Updated last year
- ☆25Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆79Updated last year
- ☆69Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- ☆30Updated 3 weeks ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆65Updated 5 months ago
- ☆28Updated 2 years ago
- ☆40Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆42Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- A tutorials suite for BioSimSpace.☆33Updated 2 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆82Updated 2 years ago
- Repository for the 2024 OpenFE industry benchmark efforts☆28Updated 3 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- 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 7 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 6 years ago
- Pocket dynamics analysis tool☆16Updated 8 months ago
- ☆21Updated 2 weeks ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated 3 months ago
- ☆39Updated 5 months ago
- Computational Chemistry Workflows☆56Updated 3 years ago
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Updated 8 months ago
- The public versio☆77Updated 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 8 months ago