A programming framework for agentic AI 🤖

High accuracy RAG for answering questions from scientific documents with citations

Chai-1, SOTA model for biomolecular structure prediction

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

Benchmark for Biophysical Sequence Optimization Algorithms

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation

Transform datasets at scale. Optimize datasets for fast AI model training.

A standard library for biological research.

Code for 'LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders'

A Modular Architecture for Deep Learning Systems

A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery (EMNLP'24)

MACE-OFF23 models

"Probabilistic Machine Learning" - a book series by Kevin Murphy

A collection of *fold* tools

Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

Fitness landscapes for antibodies

Official repository for discrete Walk-Jump Sampling (dWJS)

A concise but complete full-attention transformer with a set of promising experimental features from various papers

A collection of QM data for training potential functions

Official repository for discrete Walk-Jump Sampling (dWJS)

Protein Design with Guided Discrete Diffusion

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Code for the ProteinMPNN paper

Interaction Fingerprints for protein-ligand complexes and more

Working with molecular structures in pandas DataFrames

Explainer for black box models that predict molecule properties