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mycorason

This is a clean version of CORASON that works with genomes annotated in RAST and with genomes annotated with the tools in the FUNGIT repository.

papers_for_protein_design_using_dl

List of papers about Proteins Design using Deep Learning

pcmol

Multi-target de novo molecular generator conditioned on AlphaFold latent embeddings.

progen

Official release of the ProGen models

protein-augmentation

Comparing augmentation techniques for protein sequence classification tasks

protein_redesign

Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

proteingym

Official repository for the ProteinGym benchmarks

proteinmpnn

Code for the ProteinMPNN paper

protst

[ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

prov-gigapath

Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data

public-apis

A collective list of free APIs

pykan

Kolmogorov Arnold Networks

pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.

rfdesign

Protein hallucination and inpainting with RoseTTAFold

rfdiffusion

Code for running RFdiffusion

run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

scgpt

se3_diffusion

Implementation for SE(3) diffusion model with application to protein backbone generation

seamless_communication

Foundational Models for State-of-the-Art Speech and Text Translation

stripedhyena

Repository for StripedHyena-7B, a state-of-the-art beyond Transformer model

syny

The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.

tabpfn

Official implementation of the TabPFN paper (https://arxiv.org/abs/2207.01848) and the tabpfn package.

torchscale

Foundation Architecture for (M)LLMs

uni-dock

Uni-Dock: a GPU-accelerated molecular docking program