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☆37Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- A tutorials suite for BioSimSpace.☆25Updated 3 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Updated 4 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 4 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- 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 2 months ago
- ☆29Updated 2 weeks ago
- ☆65Updated last month
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆66Updated 2 years ago
- ☆25Updated last year
- ☆67Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 3 weeks ago
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- ☆39Updated last year
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆19Updated 3 months ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 years ago
- Computational Chemistry Workflows☆54Updated 3 years ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆70Updated 7 months ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated last month
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆56Updated 4 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆11Updated 3 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
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Updated last year