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alphacutter

This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.

alphafold

Open source code for AlphaFold.

awesome-protein-design

A curated list of awesome protein design research, software and resources.

bio_embeddings

Get protein embeddings from protein sequences

deep-protein-generation

elmo1-rhog_nanobody_design

This repository contains codes for the regeneration of figures 3b and 3g in Tam, C., Kukimoto-Niino, M., Miyata-Yabuki, Y. et al. Targeting Ras-binding domain of ELMO1 by computational nanobody design. Commun Biol 6, 284 (2023).

esm

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

fpredx

This repository contains the FPredX models for the prediction of excitation maximum, emission maximum, brightness and oligomeric state of fluorescent proteins.

ibm3202

Google Colab Tutorials for IBM3202

install_alphafold2_on_gcp_vm

machine_discussion

Data and code used in the looped-ChatGPT-BARD "machine discussion" article.

making-it-rain

Cloud-based molecular simulations for everyone

md_learning

nbx

This repository contains the NbX models for the re-ranking of nanobody–antigen binding poses.

pdb2uniprot

A Python script to map PDB ID + chain ID to UniProt ID.

preparemd

prepare AMBER files for MD simulations from a pdb file

proteinsolver

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

trdesign

trRosetta for protein design