Chao Yang's Projects
AutoDock CrankPep for peptide and disordered protein docking
Open source code for AlphaFold.
Awesome Protein Representation Learning
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER20 and OpenMM 7 simulation packages.
Blood-Brain-Barrier-Permeability prediction
Making Protein folding accessible to all!
Code for the combinatorial synthesis library variational auto-encoder (CSLVAE) as described in the paper, "An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries"
Jupyter Notebook Tutorials for Creating Chemical Space Networks
Config files for my GitHub profile.
Scan and visualize C/C++ source file dependencies.
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
Docking-Based VS
Solvent Accessible Surface calculation software for biomolecules.
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
The official implementation of the SGCN architecture.
š Super-scale your images and run experiments with Residual Dense and Adversarial Networks.
Collection of scripts / notebooks to reliably select datasets
ColabFold on your local PC
Masif seed paper repository
Molecular modeling workflows and extensions for workflow inference compiler
Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation
Interactive molecule viewer for 2D structures
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
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