hmms117

OpenDevin

🐚 OpenDevin: Code Less, Make More

SWE-agent

SWE-agent takes a GitHub issue and tries to automatically fix it, using GPT-4, or your LM of choice. It can also be employed for offensive cybersecurity or competitive coding challenges.

Verba

Retrieval Augmented Generation (RAG) chatbot powered by Weaviate

torchtune

A Native-PyTorch Library for LLM Fine-tuning

autotrain-advanced

🤗 AutoTrain Advanced

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

mPLUG-DocOwl

mPLUG-DocOwl: Modularized Multimodal Large Language Model for Document Understanding

OpenCRISPR

AI-generated gene editing systems

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

evo

Biological foundation modeling from molecular to genome scale

NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

LigandMPNN

protein-frame-flow

Fast protein backbone generation with SE(3) flow matching.

FoldFlow

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

LucaOne

The LucaOne’s code, including model code and pre-training code.

foldmason

Multiple Protein Structure Alignment at Scale with FoldMason

ProtSSN

Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2024).

PepFlowww

Full-Atom Peptide Design based on Multi-modal Flow Matching (ICML 2024)

_2024_cagiada_stability

proseLM-public

Adapting protein language models for structure-conditioned design

Scaffold-Lab

A comprehensive benchmark on the performances of multiple protein backbone generative models.

GARNET_DL

CodonMPNN

CPT

Cross-protein transfer learning for variant effect prediction

helm-gpt

HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer

ADesigner

The official implementation of the AAAI'24 paper Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer.

Pro-Prime

PRIME Model (under review)

kermut

This is the official code repository for the paper Kermut: Composite kernel regression for protein variant effects.

RDP

Random Docking p-value, a biasable significance score for PPI predictions