Brian Naughton's starred repositories

candle

Minimalist ML framework for Rust

Language:RustLicense:Apache-2.0Stargazers:15148Issues:150Issues:670

starlette

The little ASGI framework that shines. 🌟

Language:PythonLicense:BSD-3-ClauseStargazers:10058Issues:105Issues:724

marimo

A reactive notebook for Python — run reproducible experiments, execute as a script, deploy as an app, and version with git.

Language:PythonLicense:Apache-2.0Stargazers:6278Issues:29Issues:605

chai-lab

Chai-1, SOTA model for biomolecular structure prediction

Language:PythonLicense:NOASSERTIONStargazers:1001Issues:0Issues:0

PaddleHelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

Language:PythonLicense:NOASSERTIONStargazers:976Issues:25Issues:113

AlphaFold3

Open source implementation of AlphaFold3

Language:PythonLicense:Apache-2.0Stargazers:732Issues:0Issues:0

biotite

A comprehensive library for computational molecular biology

Language:PythonLicense:BSD-3-ClauseStargazers:613Issues:16Issues:174

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Language:C++License:MITStargazers:505Issues:23Issues:180

ProLIF

Interaction Fingerprints for protein-ligand complexes and more

Language:PythonLicense:Apache-2.0Stargazers:356Issues:16Issues:139

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

Language:PythonLicense:MITStargazers:340Issues:6Issues:30

DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.

Language:C++License:NOASSERTIONStargazers:262Issues:21Issues:679

Polars-Cookbook

Polars Cookbook, Published by Packt

Language:Jupyter NotebookLicense:MITStargazers:257Issues:5Issues:0

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Language:PythonLicense:Apache-2.0Stargazers:239Issues:20Issues:628

DockQ

DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models

Language:PythonLicense:MITStargazers:207Issues:8Issues:35
Language:PythonLicense:GPL-3.0Stargazers:195Issues:7Issues:238

DiffDock-PP

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

Language:Jupyter NotebookLicense:LGPL-2.1Stargazers:159Issues:4Issues:9

protpardelle

Diffusion-based all-atom protein generative model.

Language:PythonLicense:MITStargazers:153Issues:5Issues:8

alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

Language:PythonLicense:Apache-2.0Stargazers:132Issues:8Issues:15

genie2

Protein structure diffusion model for unconditional protein generation and motif scaffolding

Language:PythonLicense:Apache-2.0Stargazers:111Issues:8Issues:7
Language:PythonLicense:MITStargazers:79Issues:9Issues:28

python-rust-fst

Python bindings for Rust's fst crate

Language:PythonLicense:MITStargazers:49Issues:7Issues:9

DiffPepBuilder

Official repository for Target-Specific De Novo Peptide Binder Design with DiffPepBuilder

Language:PythonLicense:MITStargazers:39Issues:1Issues:4

pepmlm

Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

deeprank2

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

Language:PythonLicense:Apache-2.0Stargazers:33Issues:8Issues:337
Language:NextflowLicense:NOASSERTIONStargazers:24Issues:8Issues:51

LightMHC

LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks

Language:PythonLicense:NOASSERTIONStargazers:11Issues:5Issues:4

twitter95

What if Twitter was around in the year 1995?

PD-1_Fab_Diffusion

PD-1 Targeted Antibody Discovery Using AI Protein Diffusion

Language:ShellStargazers:6Issues:1Issues:0

3D-Vac

Personalized cancer vaccine design through 3D modelling boosted geometric learning.

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:3Issues:6Issues:78