Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

A variational autoencoder that directly generates the 3D coordinates of immunoglobulin protein backbones.

Accompanying Repository to TCR-TRANSLATE paper.

Hackable AlphaFold 3 inference pipeline.

Computational Chemistry Tutorials

Some tutorials on how to use AMBER simulation package. Especially for Amber22+AmberTools23.

Scripts to run AlphaFold3, Boltz-2, Chai-1, OpenFold3, Protenix & RF3 with MMseqs2 MSAs and custom templates.

⚙️ T-cell receptor sequence embedding via prototypes

Predict the structure of immune receptor proteins

Making Protein folding accessible to all!

NRGsuite is a PyMOL plugin (GUI) for FlexAID

Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse

Weighted Ensemble Data Analysis and Plotting

Papers about Structure-based Drug Design (SBDD)

An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular design

De novo drug design with deep interactome learning

Miscellaneous scripts that make life easier

Public RFDiffusionAA repo

Rifdock Library for Conformational Search

DeepRMSD+Vina is a computational framework that integrates ligand binding pose optimization and screening.

Collecting AMP MIC data from different sources, then running a GAN to output promising sequences

Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.

A collection of Jupyter Notebooks that are designed to teach life science students about deep learning.

LABODOCK: A Colab-Based Molecular Docking Tools. This fork include modified notebooks that different from its original repo

INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems