ysl-lab / CP_tutorialLinks
Introduction to cyclic peptide simulations and our group's protocols.
☆14Updated 2 years ago
Alternatives and similar repositories for CP_tutorial
Users that are interested in CP_tutorial are comparing it to the libraries listed below
Sorting:
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated last year
- ☆56Updated 9 months ago
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆65Updated 2 months ago
- ☆69Updated 2 years ago
- The public versio☆77Updated 2 years ago
- Thompson Sampling☆78Updated 8 months ago
- A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS☆123Updated last month
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Updated 8 months ago
- Fully automated high-throughput MD pipeline☆86Updated 2 weeks ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆79Updated last year
- Open-source tool to generate 3D-ready small molecules for virtual screening☆76Updated last month
- ☆43Updated 3 weeks ago
- ☆62Updated 2 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆70Updated 2 years ago
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆29Updated 6 months ago
- Simple protein-ligand complex simulation with OpenMM☆91Updated 2 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆28Updated 2 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆82Updated 2 years ago
- Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 ora…☆83Updated last month
- Python package for the analysis of natural and modified peptides using a set of modules to study their sequences☆45Updated last month
- BitBIRCH clustering algorithm☆115Updated 2 months ago
- ☆41Updated 9 months ago
- An open library to work with pharmacophores.☆48Updated 2 years ago
- Repository for SMILES-based RNNs for reinforcement learning-based de novo molecule generation☆65Updated 2 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆21Updated 7 months ago
- Cheminformatics tool that extends the decomposition of molecules into Bemis-Murcko frameworks.☆52Updated 10 months ago
- MD trajectory analysis using protein-ligand Interaction Fingerprints☆75Updated 3 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.☆60Updated 3 weeks ago
- Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)☆84Updated 5 months ago
- ☆53Updated 8 months ago