quantaosun / Dock-MD-FEP
Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertubation with OpenMM.
☆50Updated 5 months ago
Alternatives and similar repositories for Dock-MD-FEP:
Users that are interested in Dock-MD-FEP are comparing it to the libraries listed below
- ☆54Updated last year
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆55Updated last year
- ☆39Updated 6 months ago
- Computational Chemistry Workflows☆54Updated 2 years ago
- Automate MD associated calculations☆54Updated last week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆75Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆45Updated 2 months ago
- Pocket dynamics analysis tool☆12Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- The public versio☆40Updated last year
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆18Updated last month
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆14Updated this week
- AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted lig…☆37Updated this week
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- binding free energy estimator 2☆109Updated last month
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆23Updated last year
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 3 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆63Updated last week
- ☆72Updated last year
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆74Updated 7 months ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆18Updated 11 months ago
- An open library to work with pharmacophores.☆42Updated last year
- 3D ligand-based pharmacophore modeling☆48Updated last year
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆42Updated last month
- ☆25Updated last year
- Thompson Sampling☆55Updated 3 weeks ago
- ☆56Updated last year
- ☆17Updated 2 years ago
- Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3…☆47Updated 8 months ago
- Binding pocket optimization based on force fields and docking scoring functions☆30Updated last month