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:
- ☆67Updated 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.☆51Updated 6 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated 2 weeks ago
- A tutorials suite for BioSimSpace.☆27Updated 5 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆67Updated 2 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- Machine Learning model for molecular micro-pKa prediction☆43Updated last year
- ☆25Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- ☆65Updated 2 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆79Updated 2 years ago
- ☆30Updated last month
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 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 4 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated 3 weeks ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated last month
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- ☆39Updated last year
- MDANCE is a flexible n-ary clustering package for all applications.☆79Updated this week
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Pocket dynamics analysis tool☆16Updated 4 months ago
- An open library to work with pharmacophores.☆45Updated 2 years ago
- Repository for the 2024 OpenFE industry benchmark efforts☆24Updated this week
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆72Updated 8 months ago