danielnzg85

TRILL

Sandbox for Deep-Learning based Computational Protein Design

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

bioicons

A library of free open source icons for science illustrations in biology and chemistry

dyMEAN

This repo contains the codes for our paper "End-to-End Full-Atom Antibody Design"

platechain

LLMs for microplate data

FoldFlow

FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation

ProteinFlow

Versatile computational pipeline for processing protein structure data for deep learning applications.

DiffPack

Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

dash

Data Apps & Dashboards for Python. No JavaScript Required.

protpardelle

Diffusion-based all-atom protein generative model.

aligned_diffusion_bridges

Aligned Diffusion Schroedinger Bridges (UAI 2023)

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

protein_scoring

Generating and scoring novel enzyme sequences with a variety of models and metrics

conditional-flow-matching

TorchCFM: a Conditional Flow Matching library

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

aws-batch-arch-for-protein-folding

foam

Foam low-code for coders app development framework

NOS

Protein Design with Guided Discrete Diffusion

pyhamilton

Python for Hamilton liquid handling robots

holoprot

Multi-Scale Representation Learning on Proteins (NeurIPS 2021)

EigenFold

EigenFold: Generative Protein Structure Prediction with Diffusion Models

biopandas

Working with molecular structures in pandas DataFrames

molfeat

molfeat - the hub for all your molecular featurizers

automancer

Automancer is a software application that enables researchers to design, automate, and manage their experiments.

ColabDesign

Making Protein Design accessible to all via Google Colab!

ProteinFlow-models

Modifications of ProteinMPNN trained on ProteinFlow data

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

Ankh

Ankh: Optimized Protein Language Model