tony-blake / MD-Simulation
A Generalised workflow for obtaining protein and peptide molecular structures, docking the peptide into the protein and running a molecular dynamic simulation over a large number of trajectories.
☆11Updated 3 months ago
Alternatives and similar repositories for MD-Simulation:
Users that are interested in MD-Simulation are comparing it to the libraries listed below
- Parallelized Open Babel & Autodock suite Pipeline☆24Updated 7 years ago
- An MPI based parallel implementation of Autodock Vina☆16Updated 5 years ago
- Python code to automatically interact with PDBePISA web server☆10Updated 2 years ago
- MD pharmacophores and virtual screening☆33Updated last year
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆20Updated 5 years ago
- Analysis of contacts in molecular dynamics trajectories☆42Updated 5 years ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆29Updated 10 months ago
- Self explained tutorial for molecular dynamics simulation using gromacs☆23Updated 5 months ago
- PyMOL Plugin for displaying polar contacts☆17Updated 6 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 4 years ago
- ATTRACT program suite for macromolecular docking (protein-protein, protein-nucleic acid, protein-peptide)☆16Updated last year
- a pipeline for running MD simulations in the presence of probe molecules for druggability assessment☆12Updated last year
- This repo contains the collection of codes to find designer interfacial mutations☆17Updated last year
- Google Colab notebooks for running molecular dynamics simulations with GROMACS☆30Updated last year
- Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file☆32Updated last year
- A place to store and edit the lab handbook for UCL courses that involve the use of open source tools in molecular docking.☆22Updated 2 years ago
- Automated construction of protein chimeras and their analysis.☆14Updated last year
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆19Updated 3 years ago
- The code for the QuickVina homepage.☆33Updated 2 years ago
- Tools to calculate descriptors from molecular dynamics and it's application to predict drug resistance.☆13Updated 2 years ago
- Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.☆35Updated 4 years ago
- Cyclic-peptide - protein complexes benchmark and associated scripts and data☆11Updated 7 months ago
- PyDock Tutorial☆30Updated 6 years ago
- development repository for PyInteraph2☆22Updated last month
- ☆18Updated 3 years ago
- ☆12Updated 4 years ago
- Machine learning model for predicting Human Oral Bioavailability☆13Updated 3 years ago
- Fraction of Common Contacts Clustering Algorithm for Protein Structures☆26Updated 3 years ago
- PCA and normal mode analysis of proteins☆17Updated 11 months ago
- A Consensus Docking Plugin for PyMOL☆72Updated 10 months ago