Implementation of Alphafold 3 in Pytorch

Making Protein Design accessible to all via Google Colab!

Practical Cheminformatics Tutorials

In silico directed evolution of peptide binders with AlphaFold

Scoring of shape and ESP similarity with RDKit

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Code and data used in https://doi.org/10.1101/2021.08.01.454656

Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

Implementation of Lilly Medchem Rules - J Med Chem 2012

Peptide Virtual Screening Pipeline

Full-Atom Peptide Design based on Multi-modal Flow Matching (ICML 2024)

Multiple Protein Structure Alignment at Scale with FoldMason

Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

pyPept: a python library to generate atomistic 2D and 3D representations of peptides

PARCE version 1.0

implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking

A curated list of Python packages related to chemistry

Rifdock Library for Conformational Search

Using Rotamer Interaction Fields from RIFGen/Dock in python

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

High-speed Large Language Model Serving on PCs with Consumer-grade GPUs

MSAGPT

The LucaOne’s code, including model code and pre-training code.