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alphafold-multimer

biosensor_design-workflow

This is a manual for BioSensor_design workflow script and an example

cds-variant-calculator-and-machine-learning-for-multigene-pathway-optimization

CDS variant calculator and machine learning for multigene pathway optimization

chemprop

Message Passing Neural Networks for Molecule Property Prediction

chroma

A generative model for programmable protein design

conplex

Adapting protein language models and contrastive learning for highly-accurate drug-target interaction prediction.

deepdirect

deepmutsol

deeppurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

dlkcat

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

drugchat

DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs

esm

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

esm3

gene-diversifier

gpt-pilot

Dev tool that writes scalable apps from scratch while the developer oversees the implementation

graphsol

Code of our JC paper: "Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map"

lineardesign

The LinearDesign mRNA design software from Baidu.

llama-factory

Easy-to-use LLM fine-tuning framework (LLaMA, BLOOM, Mistral, Baichuan, Qwen, ChatGLM)

makeyourownneuralnetwork

Code for the Make Your Own Neural Network book

oareactdiff

An object-aware diffusion model for generating chemical reactions

parsnip

Sequence-based protein solubility predictor

pdb2fasta

implementing PDB to FASTA file format conversion in multiple languages

pon-sol2

The source code and data of PON-Sol2.

postcat

Postcat 是一个可扩展的 API 工具平台。集合基础的 API 管理和测试功能，并且可以通过插件简化你的 API 开发工作，让你可以更快更好地创建 API。An extensible API tool.

prostata

protein-ligand-gnn

This repository contains the code for the work on protein-ligand interaction with GNNs and XAI

protein_stability_design-workflow

This is a process of protein stability modification designed by exploring weak regions of the protein.

proteinmpnn

Code for the ProteinMPNN paper

pu-epp

This repository contains the positive-unlabeled learning-based enzyme promiscuity prediction model as described in the paper Deep learning Enables Rapid Identification of Mycotoxin-degrading Enzymes.

rfdiffusion

Code for running RFdiffusion