Zuricho

Zuricho's Stars

• facebookresearch/flow_matching

  A PyTorch library for implementing flow matching algorithms, featuring continuous and discrete flow matching implementations. It includes practical examples for both text and image modalities.

  Language:Python1.5k58

• AbSciBio/igdesign

  Language:Python184

• opencobra/cobrapy

  COBRApy is a package for constraint-based modeling of metabolic networks.

  Language:Python474218

• microsoft/markitdown

  Python tool for converting files and office documents to Markdown.

  Language:Python26.7k1k

• sagiweizmann/MusicEncrypt

  Music Encryption with .wav files , GUI Made in tkinter.

  Language:Python2

• amyxlu/cheap-proteins

  Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. https://www.biorxiv.org/content/10.1101/2024.08.06.606920v1

  Language:Python987

• MrOlm/drep

  Rapid comparison and dereplication of genomes

  Language:Python26938

• genbio-ai/AIDO

  AI-Driven Digital Organism (AIDO) is a system of multiscale foundation models for predicting, simulating and programming biology at all levels

  314

• wavmark/wavmark

  AI-based Audio Watermarking Tool

  Language:Python23532

• cddlab/alphafold3_tools

  Toolkit for alphafold3 input and output files

  Language:Python457

• zhangliang-sys/PRO-DREAM

  A Deep Retrieval-Enhanced Meta-learning Framework for Enzyme optimum pH Prediction

  Language:Python5

• ginnm/ThermoFormer

  Source code of ThermoFormer (Foundation Models for Science Workshop, NeurIPS 2024.)

  Language:Python4

• biocheming/AF3_mmseqs2

  Alphafold3 using mmseqs2-gpu for sequence query

  Language:Python10

• DeepGraphLearning/S3F

  Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)

  Language:Python181

• NVIDIA/NeMo

  A scalable generative AI framework built for researchers and developers working on Large Language Models, Multimodal, and Speech AI (Automatic Speech Recognition and Text-to-Speech)

  Language:Python12.5k2.6k

• meilerlab/HyperMPNN

  HyperMPNN ‒ A general strategy to design thermostable proteins learned from hyperthermophiles

  Language:Jupyter Notebook428

• luost26/tinyfold

  :rocket: MIT 6.5940 TinyML Final Project: Optimization and Edge Deployment of ESMFold

  Language:Python3

• NVIDIA/cuEquivariance

  cuEquivariance is a math library that is a collective of low-level primitives and tensor ops to accelerate widely-used models, like DiffDock, MACE, Allegro and NEQUIP, based on equivariant neural networks.

  Language:Python1476

• moshi4/pyMSAviz

  MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

  Language:Python10416

• coderlemon17/LemonScripts

  Here is the repo for public scripts.

  Language:Jupyter Notebook7

• chao1224/NeuralMD

  NeuralMD for protein-ligand binding simulation

  Language:Python101

• alirezaomidi/AFM-IDR

  Official repo for paper "AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions"

  Language:Python152

• clementchadebec/benchmark_VAE

  Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

  Language:Python1.8k167

• DreamFold/FoldFlow

  FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation

  Language:Jupyter Notebook20011

• ci-lab-cz/streamd

  Automate MD associated calculations

  Language:Python5114

• ElanaPearl/InterPLM

  Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

  Language:Python1347

• jwohlwend/boltz

  Official repository for the Boltz-1 biomolecular interaction model

  Language:Python1.4k163

• linsalrob/ComputationalGenomicsManual

  Robs manual for the computational genomics and bioinformatics class.

  Language:HTML22861

• samsledje/philharmonic

  Decoding the functional networks of non-model organisms

  Language:Jupyter Notebook5

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5.6k665