"Rewriting protein alphabets with language models"

Fast protein structure searching or your money back

A lightweight, fast pocket finder in Python.

Extremely fast Query Engine for DataFrames, written in Rust

Profluent-E1 family of Protein Encoder Models

A fully open source biomolecular structure prediction model based on AlphaFold3

A tiny scalar-valued autograd engine and a neural net library on top of it with PyTorch-like API

Neural Networks: Zero to Hero

The best ChatGPT that $100 can buy.

Platonic Transformers: A Solid Choice For Equivariance

Potts model-based protein sequence design

Implementation of Vision Transformer, a simple way to achieve SOTA in vision classification with only a single transformer encoder, in Pytorch

A generalized computational framework for biomolecular modeling.

PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

Efficient implementatin of ESM family.

A LLM trained only on data from certain time periods to reduce modern bias

Trainable subnetworks to disentangle structure knowledge in pretrained protein language models

Metrics to evaluate distributional coverage of generative models of protein structures.

A Python implementation of global optimization with gaussian processes.

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation

Curated list of interactive ML demos

MiniFold: Simple, Fast and Accurate Protein Structure Prediction

Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

Protein Engineering via Exploration of an Energy Landscape