ccchai1

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

score_sde_pytorch

PyTorch implementation for Score-Based Generative Modeling through Stochastic Differential Equations (ICLR 2021, Oral)

AlphaFold3

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

chemprop

Message Passing Neural Networks for Molecule Property Prediction

dubportal

An integrative resource for deubiquitinating enzymes (DUBs) served at https://labsyspharm.github.io/dubportal

cryptosite

Library for prediction of cryptic binding sites

Score2Analysis

Scripts for producing figures included in Second-generation map of genetic vulnerabilities in cancer cells

DiffDockHPC

DiffDock implementation that adds support for HPC execution using Slurm and Singularity

esm

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

DiffDock-PP

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

DiffLinker

DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design

Orphadata_aggregated

Provided files are a partial extraction of the Orphanet knowledge base on Rare Diseases

pandas-ai

Chat with your database (SQL, CSV, pandas, polars, mongodb, noSQL, etc). PandasAI makes data analysis conversational using LLMs (GPT 3.5 / 4, Anthropic, VertexAI) and RAG.

ChemTS

Molecule Design using Monte Carlo Tree Search with Neural Rollout

BioGPT

nglview

Jupyter widget to interactively view molecular structures and trajectories

attention-is-all-you-need-pytorch

A PyTorch implementation of the Transformer model in "Attention is All You Need".

nlp-tutorial

Natural Language Processing Tutorial for Deep Learning Researchers

book

The Rust Programming Language

PGMG

The official PyTorch implementation of PGMG: A Pharmacophore-Guided Deep Learning Approach for Bioactive Molecule Generation.

OpenFermion-FQE

The Fermionic Quantum Emulator (FQE) is a fermionic simulation research tool specializing in quantum circuits emulating fermion dynamics.

medical-data

LAIDD2022-math-for-ML

baseballr

A package written for R focused on baseball analysis. Currently in development.

gpu-jupyter

Leverage the flexibility of Jupyterlab through the power of your NVIDIA GPU to run your code from Tensorflow and Pytorch in collaborative notebooks on the GPU.

gpu-jupyter

GPU-Jupyter: Leverage the flexibility of Jupyterlab through the power of your NVIDIA GPU to run your code from Tensorflow and Pytorch in collaborative notebooks on the GPU.

gromacs

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

django

The Web framework for perfectionists with deadlines.

Drug-Repurposing-in-KNIME

An Integrative Drug Repurposing Pipeline using KNIME and Programmatic Data Access: A case study on COVID-19 Data