quantaosun / Ambertools-OpenMM-MD
Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.
☆30Updated last month
Related projects: ⓘ
- Google Colab notebooks for running molecular dynamics simulations with GROMACS☆21Updated 11 months ago
- Docking Tutorial Using Autodock Vina version 1.2.3 (2021) and AutoDock-GPU Version 1.5.3☆25Updated 3 weeks ago
- Analysis of contacts in molecular dynamics trajectories☆41Updated 4 years ago
- Machine learning model for predicting Human Oral Bioavailability☆13Updated 2 years ago
- model builder for molecular dynamics simulations☆13Updated last year
- Academic license pre-required. While FEP Plus charge you 100,000 USD per year. Here comes the FEP-Minus, it is a Schrodinger FEP Plus ide…☆17Updated last month
- The official open-source repository for AutoMolDesigner, an easy-to-use Python application dedicated to automated molecular design.☆18Updated 4 months ago
- Automatic gromacs protocol from preparation to production with ligand parametrization through☆56Updated 3 months ago
- MD pharmacophores and virtual screening☆31Updated 9 months ago
- dockECR: open consensus docking and ranking protocol for virtual screening of small molecules☆24Updated 2 years ago
- Use AutoDock for Ligand-based Virtual Screening☆19Updated last month
- A place to store and edit the lab handbook for UCL courses that involve the use of open source tools in molecular docking.☆20Updated 2 years ago
- Scores for Hydrophobicity and Charges based on SASAs☆20Updated this week
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆23Updated 2 months ago
- DiffDock implementation that adds support for HPC execution using Slurm and Singularity☆23Updated this week
- An open-source library for the analysis of protein interactions.☆29Updated 2 years ago
- Fraction of Common Contacts Clustering Algorithm for Protein Structures☆25Updated 3 years ago
- ☆18Updated 2 years ago
- development repository for PyInteraph2☆21Updated last year
- ☆19Updated last year
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆50Updated 2 months ago
- a universal framework for computational protein design☆34Updated last year
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆42Updated 3 years ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 4 years ago
- MMTSB Tool Set☆29Updated last month
- A Consensus Docking Plugin for PyMOL☆63Updated 3 months ago
- pyKVFinder: Python-C parallel KVFinder☆19Updated last week
- Collection of scripts that integrates docking, virtual screening, similarity and molecular modeling programs.☆24Updated last month
- This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua☆23Updated 7 months ago
- ☆82Updated last year