Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

Joint sequence and structure generation with RoseTTAFold sequence space diffusion

Derivative-Free Guidance in Diffusion Models with Soft Value-Based Decoding. For controlled generation in DNA, RNA, proteins, molecules (+ images)

Code for the paper https://arxiv.org/abs/2402.04997

List of computational protein design research labs

Official repository of ReactZyme

Supporting code for our paper "Protein Sequence Modelling with Bayesian Flow Networks"

List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning

Deep learning framework for protein sequence design from a backbone scaffold that can leverage the molecular context including non-protein entities.

MMseqs2: ultra fast and sensitive search and clustering suite

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Reaction-Conditioned Virtual Screening of Enzymes

Practical Cheminformatics Tutorials

Official repository for discrete Walk-Jump Sampling (dWJS)

A beautiful, simple, clean, and responsive Jekyll theme for academics

CLEAN: a contrastive learning model for high-quality functional prediction of proteins

RXN for biochemical reactions

An NLP-inspired chemical reaction fingerprint based on basic set arithmetic.

Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Multi-modal Molecule Structure-text Model for Text-based Editing and Retrieval, Nat Mach Intell 2023 (https://www.nature.com/articles/s42256-023-00759-6)

the most goated babel plugin

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Code for running RFdiffusion

A statistical toolkit for scientific discovery using machine learning

SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.

Degenerate Codon Design

A compilation of deep learning methods for protein design