Contains the digitized chapters of the book "System Design with Ada"

AutoML system for building trustworthy peptide bioactivity predictors

Sidechain conditioning and modeling for full-atom protein sequence design

Pen and paper exercises in machine learning

It's a package for evaluation of predicted poses, right?

Code for ColabDock paper

List of papers about Proteins Design using Deep Learning

Protein Ligand INteraction Dataset and Evaluation Resource

PINDER: The Protein INteraction Dataset and Evaluation Resource

Creating a diffusion model from scratch in PyTorch to learn exactly how they work.

Protein structure diffusion model for unconditional protein generation and motif scaffolding

A Rust library for calculating the SASA for a protein. 5x faster than Freesasa. Based on the Shrake & Rupley algorithm.

[ACL 2024] ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training

Developing classification models for DNA-Binding proteins through machine learning and large language models

Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.

Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation

Deep Generative Models: Diffusion Models for Molecule Generation

Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"

An antibody-specific language model focusing on NGL prediction

Implementation code for the paper "Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport"

Transformer-based model for chemical reactions

Structure-conditioned masked language modeling for protein sequence design

FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.

Sandbox for Deep-Learning based Computational Protein Design

A rust crate to interface with the freesasa library for protein surface area calculations

De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments