AaranWang

AbDesign_for_enzymes

Scripts and data to run AbDesign as described in Tools for protein science 2021

alphafold-deepmind

Open source code for AlphaFold.

alphafold-kuixu

Install alphafold on the local machine, get out of docker.

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

awesome-AI4ProteinConformation-MD

List of protein conformations and molecular dynamics using generative artificial intelligence and deep learning

CADENZ

Code and data for the CADENZ paper

ColabFold

Making Protein folding accessible to all via Google Colab!

conv_arithmetic

A technical report on convolution arithmetic in the context of deep learning

correlationplus

A Python package to calculate, visualize and analyze correlation maps of proteins.

diffusers

🤗 Diffusers: State-of-the-art diffusion models for image and audio generation in PyTorch

AaranWang/alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

AaranWang/awesome-AI4ProteinConformation-MD

List of protein conformations and molecular dynamics using generative artificial intelligence and deep learning

AaranWang/CADENZ

Code and data for the CADENZ paper

AaranWang/correlationplus

A Python package to calculate, visualize and analyze correlation maps of proteins.

AaranWang/diffusers

🤗 Diffusers: State-of-the-art diffusion models for image and audio generation in PyTorch

AaranWang/htFuncLib

AaranWang/ILearnDeepLearning.py

This repository contains small projects related to Neural Networks and Deep Learning in general. Subjects are closely linekd with articles I publish on Medium. I encourage you both to read as well as to check how the code works in the action.

AaranWang/papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

AaranWang/presentations

Slides from my talks

AaranWang/ProteinGAN

AaranWang/esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

AaranWang/ESM-AA

AaranWang/esm3

AaranWang/foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

AaranWang/fs-mutant

A few-shot learning dataset for protein mutants mining

AaranWang/heme_binder_diffusion

AaranWang/P450Diffusion

P450Diffusion: A tool for designing P450 sequences based on diffusion model

AaranWang/ProSST

Code for ProSST: A Pre-trained Protein Sequence and Structure Transformer with Disentangled Attention.

AaranWang/protein_scoring

Generating and scoring novel enzyme sequences with a variety of models and metrics

AaranWang/ProteinGym

Official repository for the ProteinGym benchmarks

AaranWang/ProteinMPNN

Code for the ProteinMPNN paper

AaranWang/rf_diffusion_all_atom

Public RFDiffusionAA repo

AaranWang/RFDesign

Protein hallucination and inpainting with RoseTTAFold

AaranWang/RFdiffusion

Code for running RFdiffusion

AaranWang/RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

AaranWang/RoseTTAFold-All-Atom

AaranWang/SaProt

Saprot: Protein Language Model with Structural Alphabet

AaranWang/SaprotHub

SaprotHub: Making Protein Modeling Accessible to All Biologists

AaranWang/trdesign-motif

Codebase for our preprint using trRosetta to design proteins with discontinuous functional sites, found here: https://www.biorxiv.org/content/10.1101/2020.11.29.402743v1.abstract

AaranWang/trRosetta

A package to predict protein inter-residue geometries from sequence data