Wang-Lin-boop / AutoMD
Easy to get started with molecular dynamics simulation.
☆39Updated last week
Related projects ⓘ
Alternatives and complementary repositories for AutoMD
- Scripts for virtual screening, cross docking and protein relax using Schrödinegr and Rosetta☆58Updated last month
- Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including vi…☆41Updated this week
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆47Updated 3 months ago
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆62Updated 3 months ago
- some scripts for analysis of MD and CADD. And some tutorials.☆52Updated 3 months ago
- Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, …☆51Updated 3 weeks ago
- ☆39Updated 4 months ago
- ☆50Updated 11 months ago
- FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.☆48Updated 10 months ago
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆95Updated 2 weeks ago
- Graph variational encoders for drug engineering and potentiation☆26Updated last year
- 3D-MCTS: A general structure-based molecule generation method with MCTS.☆40Updated 4 months ago
- binding free energy estimator 2☆108Updated last week
- ☆16Updated 2 years ago
- Pocket dynamics analysis tool☆12Updated 3 months ago
- CHAPERONg: An automated pipeline for GROMACS MD simulations and trajectory analyses☆36Updated 2 months ago
- DeepRMSD+Vina is a computational framework that integrates ligand binding pose optimization and screening.☆38Updated 10 months ago
- LABODOCK: A Colab-Based Molecular Docking Tools☆40Updated 9 months ago
- Official repo of "CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training…☆70Updated 3 months ago
- Simple protein-ligand complex simulation with OpenMM☆73Updated last year
- De novo drug design with deep interactome learning☆28Updated 5 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆53Updated last year
- Codes and scripts for "An artificial intelligence accelerated virtual screening platform for drug discovery"☆38Updated last week
- implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking☆51Updated 3 weeks ago
- Python package to facilitate the use of popular docking software☆14Updated last year
- ☆37Updated 10 months ago
- ☆93Updated 3 months ago
- AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted lig…☆35Updated last week
- Automatic gromacs protocol from preparation to production with ligand parametrization through☆59Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆74Updated last year