Jianxiang Shi's repositories
AbEpiTope-1.0
AbEpiTope-1.0 is a computational tool that features two scores: AbEpiScore-1.0, designed for assessing the accuracy of modelled AbAg interfaces, and AbEpiTarget-1.0, optimised for selecting the antibody most likely to bind a given antigen.
AlphaFold3
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
antibody-affinity
Antibody affinity modeling
AntiFold
Improved antibody structure-based design using inverse folding
awesome-vdj
📚 Tools and databases for analyzing HLA and VDJ genes.
casanovo
De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
chai-lab
Chai-1, SOTA model for biomolecular structure prediction
cherry-studio
🍒 Cherry Studio is a desktop client that supports for multiple LLM providers. Support deepseek-r1
DiaNN
DIA-NN - a universal automated software suite for DIA proteomics data analysis.
EnzymeFlow
Official repository of EnzymeFlow
evo2
Genome modeling and design across all domains of life
EvolvePro
This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.
EvolveX
EvolveX, a de novo antibody computational design pipeline.
GENzyme
Official repository of GENzyme
GeoAB
This is the official repository of paper - GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation (ICML2024)
iptv
Collection of publicly available IPTV channels from all over the world
locuaz
Antibody optimization platform
neofox
Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
NeoNectin
Codes Used for NeoNectin Development
NetTCR-2.2
Sequence-based prediction of peptide-TCR interactions using paired chain data
papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
prodigy
Predict the binding affinity of protein-protein complexes from structural data
ReactZyme
Official repository of ReactZyme
scRNAtoolVis
Useful functions to make your scRNA-seq plot more cool!
SEMAi
Spatial Epitope Modeling with Artificial intelligence (SEMA)
TCR-BCR-seq-analysis
T/B cell receptor sequencing analysis notes
tfold
open source code for Tencent tFold
zed
Code at the speed of thought – Zed is a high-performance, multiplayer code editor from the creators of Atom and Tree-sitter.