jusjosgra

ALife

Artificial Life simulations

LatProtRL

[ICML 24] Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space

ProteinMPNN

Code for the ProteinMPNN paper

protein-dpo

Aligning protein generative models with experimental fitness

ComfyUI-audio

some generative audio tools for ComfyUI

AnimateDiff

Official implementation of AnimateDiff.

DSMBind

UniRep

UniRep model, usage, and examples.

text-generation-inference

Large Language Model Text Generation Inference

scifAI

scifAI: An explainable AI python framework for the analysis of multi-channel imaging data

af2bind_prod

ProteinGym

Official repository for the ProteinGym benchmarks

atlas

A brain for self-driving laboratories

olympus

Olympus: a benchmarking framework for noisy optimization and experiment planning

ipyMolecularNodes

molecular plots in Jupyter, powererd by Blender Geometry Nodes

LLM-Agent-Paper-List

The paper list of the 86-page paper "The Rise and Potential of Large Language Model Based Agents: A Survey" by Zhiheng Xi et al.

deap

Distributed Evolutionary Algorithms in Python

DeCOIL

A computational method to optimize degenerate codons for synthesizing an informed combinatorial mutagenesis protein variant library

BALM

Inference code for BALM

EvoPlay

MLDE

A machine-learning package for navigating combinatorial protein fitness landscapes.

AntiBERTy

Antibody-specific masked language model

ai-town

A MIT-licensed, deployable starter kit for building and customizing your own version of AI town - a virtual town where AI characters live, chat and socialize.

biotransfer

Machine learning-driven antibody design

text-generation-webui

A Gradio web UI for Large Language Models.

efficient-evolution

Efficient evolution from protein language models

Sapiens

Sapiens is a human antibody language model based on BERT.

ColabFold

Making Protein folding accessible to all!

antiberty-pytorch

An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.

ddpm-ipa-protein-generation

Implementation of the DDPM + IPA (invariant point attention) for protein generation, as outlined in the paper "Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models"