JoaoRodrigues / openmm_scripts
Collection of Python scripts to setup and run simulations with OpenMM
☆17Updated 4 years ago
Alternatives and similar repositories for openmm_scripts:
Users that are interested in openmm_scripts are comparing it to the libraries listed below
- Computational Chemistry Workflows☆54Updated 2 years ago
- ☆25Updated last year
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 4 years ago
- ☆13Updated last year
- ☆28Updated this week
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated 3 weeks ago
- RF-Score-VS binary☆31Updated 6 years ago
- A knowledge-based method for determining small molecule binding "hotspots".☆35Updated last year
- Fully automated high-throughput MD pipeline☆60Updated this week
- Tutorial to build AMBER compatable protein+lipid systems☆15Updated 8 years ago
- ☆16Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- ☆59Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- A collections of scripts for working molecular dynamics simulations☆43Updated 11 months ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆20Updated 5 years ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆47Updated this week
- Updated version of Silicos-it's shape-based alignment tool☆41Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆36Updated 9 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆48Updated last month
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆19Updated 9 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆18Updated 8 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- An open library to work with pharmacophores.☆45Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆27Updated 3 years ago
- A tutorials suite for BioSimSpace.☆25Updated this week
- ☆34Updated last year
- Machine Learning Boosted Docking (HASTEN): Accelerate Structure-based Virtual Screening☆39Updated last year