vis-yyin

antiref

AntiRef: reference clusters of human antibody sequences

AVIDa-hIL6

Code for NeurIPS 2023 paper "AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions"

AbAgIntPre

AbAgIntPre webserver source code

PICH

Priority Index Approach to Clonal Hematopoiesis

Frame2seq

Structure-conditioned masked language modeling for protein sequence design

sparse

Sparse multi-dimensional arrays for the PyData ecosystem

Snippets-for-ColabFold

A collections of snippets for working with ColabFold

pyrosetta-help

Some scripts that I keep using over and over.

AlphaRED

AlphaFold-initiated replica exchange protein docking

supervenn

supervenn: precise and easy-to-read multiple sets visualization in Python

SPACE2

Tool for rapid clustering of antibody models by the structure of their CDRs.

DockQ

DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol

KarmaLoop

Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop

ColabFold

Making Protein folding accessible to all!

localcolabfold

ColabFold on your local PC

dyMEAN

This repo contains the codes for our paper "End-to-End Full-Atom Antibody Design"

AttnPacker

Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

FvHallucinator

Machine-learning-for-proteins

Listing of papers about machine learning for proteins.

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

nanobody-polyreactivity

Polyreactivity Website

diffab

✌🏻 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (NeurIPS 2022)

rgn2

OmegaFold

OmegaFold Release Code

IgFold

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

ImmuneBuilder

Predict the structure of immune receptor proteins

kasearch

KA-Search: Rapid and exhaustive sequence identity search of known antibodies

esm

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

ScanNet