ysl-lab / CP_tutorial
Introduction to cyclic peptide simulations and our group's protocols.
☆11Updated last year
Alternatives and similar repositories for CP_tutorial:
Users that are interested in CP_tutorial are comparing it to the libraries listed below
- ☆63Updated 6 months ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆18Updated 11 months ago
- Automate MD associated calculations☆54Updated 2 weeks ago
- ☆33Updated 9 months ago
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆20Updated this week
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆23Updated last year
- Thompson Sampling☆55Updated 3 weeks ago
- The public versio☆40Updated last year
- 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
- Simple protein-ligand complex simulation with OpenMM☆74Updated last year
- ☆54Updated last year
- Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design☆43Updated last week
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆18Updated last month
- Implementation of CycPeptMP, an accurate and efficient model for predicting the membrane permeability of cyclic peptides☆16Updated last month
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- Computational Chemistry Workflows☆54Updated 2 years ago
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆14Updated this week
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- ☆21Updated 8 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Binding pocket optimization based on force fields and docking scoring functions☆30Updated last month
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆42Updated last month
- ☆56Updated last year
- Automated Adaptive Absolute alchemical Free Energy calculator☆79Updated last week
- Convert coarse-grained protein structure to all-atom model☆36Updated 6 months ago
- ☆11Updated last year
- A python module to plot secondary structure schemes☆25Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- an ultra-fast and accurate program for deterministic protein sidechain packing☆28Updated last month