Jianxiang Shi's repositories
Abalign
A visualization software for antibody multi sequence alignment
AbLang
AbLang: A language model for antibodies
ABlooper
Tool for modelling the CDRs of antibodies
ANARCI
Antibody Numbering and Antigen Receptor ClassIfication
antibody-design
Modeling antibody design based on antibody and antigen information. Will also look at other existing methods for modeling antibodies.
aspera-cli
IBM Aspera CLI
BioPhi
BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.
chatgpt_academic
科研工作专用ChatGPT拓展，特别优化学术Paper润色体验，支持自定义快捷按钮，支持自定义函数插件，支持markdown表格显示，Tex公式双显示，代码显示功能完善，新增本地Python/C++/Go项目树剖析功能/项目源代码自译解能力，新增PDF和Word文献批量总结功能/PDF论文全文翻译功能
cif2pdb
Convert mmCIF to PDB protein structure file format
clash
A rule-based tunnel in Go.
CodeFormer
[NeurIPS 2022] Towards Robust Blind Face Restoration with Codebook Lookup Transformer
CodonHumanization
A Novel Approach to Codon Optimization Based on Machine Learning and Genetic Algorithm
ColabFold
Making Protein folding accessible to all!
ConPLex
Adapting protein language models and contrastive learning for highly-accurate drug-target interaction prediction.
deephlapan
A deep learning approach for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC
discotope3_web
DiscoTope-3.0: Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations
foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
IgFold
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
IgLM
Generative Language Modeling for Antibody Design
ImmuneBuilder
Predict the structure of immune receptor proteins
languagetool
Style and Grammar Checker for 25+ Languages
ReprogBERT
Code for ICML 2023 paper "Reprogramming Pretrained Language Models for Antibody Sequence Infilling"
RFDesign
Protein hallucination and inpainting with RoseTTAFold
rosetta-antibody-ddgs
Repository for the JHU Rosetta Commons REU project I completed during the summer of 2022 in the Whitehead Lab at CU Boulder.
scDrug
scDrug: From scRNA-seq to Drug Repositioning
TorchProteinLibrary
PyTorch library of layers acting on protein representations