purnawanpp / plants
Tutorial using PLANTS (Protein-Ligand ANTSystem)
☆8Updated 6 months ago
Alternatives and similar repositories for plants:
Users that are interested in plants are comparing it to the libraries listed below
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆56Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆43Updated 3 years ago
- Different run and analysis scripts as described in the research guides.☆12Updated 2 years ago
- ☆39Updated 6 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆23Updated last year
- Machine Learning model for molecular micro-pKa prediction☆38Updated 4 months ago
- Automate MD associated calculations☆53Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- 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
- ☆54Updated last year
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆16Updated 5 months ago
- ☆25Updated last year
- ☆73Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆34Updated 6 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆20Updated 3 weeks ago
- The public versio☆41Updated last year
- Computational Chemistry Workflows☆54Updated 2 years ago
- ☆29Updated 3 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 5 months ago
- Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, acc…☆23Updated 10 months ago
- ☆13Updated last month
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- The official repository of Uni-pKa☆43Updated last month
- Thompson Sampling☆55Updated last month
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆74Updated 7 months ago
- ☆26Updated 7 months ago