Shirhaha

strong-docking-baseline

Code accompanying our blog post on a stronger docking baseline for Alpha Fold 3 docking

esm

practical_cheminformatics_tutorials

Practical Cheminformatics Tutorials

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

PocketFlow

an autoregressive flow model incorporated with chemical acknowledge for generating drug-like molecules inside protein pockets

Awesome_BigData_AI_DrugDiscovery

A collection of resources useful for leveraging big data and AI for drug discovery. It mainly serves as an orientation for new lab folks. It may be biased towards my lab interest.

start-llms

A complete guide to start and improve your LLM skills in 2024 with little background in the field and stay up-to-date with the latest news and state-of-the-art techniques!

s2orc-doc2json

Parsers for scientific papers (PDF2JSON, TEX2JSON, JATS2JSON)

codellama

Inference code for CodeLlama models

TEIM

TEIM: TCR-Epitope Interaction Modeling

pops

pqsar2cpd

pqsar2cpd is a deep learning algorithm for translation of activity profiles into novel molecules.

biocypher

A unifying framework for biomedical research knowledge graphs

tautomatic

Facile exploration and assessment of chemical tautomer space.

scaffold_hopping_whales

Code to perform scaffold hopping and virtual screening using WHALES descriptors.

data-centric-AI

A curated, but incomplete, list of data-centric AI resources.

RxnScribe

A Sequence Generation Model for Reaction Diagram Parsing

TCRdock

python tools for TCR:peptide-MHC modeling and analysis

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

molbloom

Molecular bloom filter tool

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

DECIMER-Image_Transformer

DECIMER: Deep Learning for Chemical Image Recognition using Efficient-Net V2 + Transformer

paper-reading

深度学习经典、新论文逐段精读

bioc

Data structures and code to read/write BioC XML and Json.

hydrophobic_patches

MuskAPI

Elon Musk's tweets, as a service.

pubmed_parser

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

following-instructions-human-feedback

OPERA

Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.

AIDTox