Jianxiang Shi's repositories
AlphaFold3
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
antibody-affinity
Antibody affinity modeling
ANTIPASTI
ANTIPASTI (ANTIbody Predictor of Affinity from STructural Information) is a Deep Learning model that predicts the binding affinity of antibodies from their three-dimensional structure.
bypy
Python client for Baidu Yun (Personal Cloud Storage) 百度云/百度网盘Python客户端
ColabDesign
Making Protein Design accessible to all via Google Colab!
DiffDock-PP
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
GeoAB
This is the official repository of paper - GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation (ICML2024)
Graphinity
Graphinity: Equivariant Graph Neural Network Architecture for Predicting Change in Antibody-Antigen Binding Affinity
grok-1
Grok open release
locuaz
Antibody optimization platform
mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
multiPrime
multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))
NeoNectin
Codes Used for NeoNectin Development
NetTCR-2.2
Sequence-based prediction of peptide-TCR interactions using paired chain data
NGS-PrimerPlex
NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design
papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
PMPrimer
Automatically design multiplex PCR primer pairs for diverse templates
prodigy
Predict the binding affinity of protein-protein complexes from structural data
RFdiffusion
Code for running RFdiffusion
scRNAtoolVis
Useful functions to make your scRNA-seq plot more cool!
SelfPAD
The official implementation of "Improving Antibody Humanness Prediction using Patent Data".
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
TRUST4
TCR and BCR assembly from RNA-seq data