johnnytam100

Johnny Tam's repositories

AlphaCutter

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

Language:PythonMIT12 1 3

awesome-protein-design

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

11 30

pdb2uniprot

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

Language:Python11 1 2

FPredX

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

Language:Python3 1 1

NbX

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

Language:Python3 10

proteinsolver

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

Language:Jupyter NotebookMIT100

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.

Language:Jupyter NotebookAFL-3.0100

PyRosetta.notebooks

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

Language:Jupyter NotebookMIT100

alphafold

Open source code for AlphaFold.

Language:PythonApache-2.0000

bio_embeddings

Get protein embeddings from protein sequences

Language:HTMLMIT000

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).

Language:Jupyter Notebook010