johnnytam100
Tam is a bioinformatician with 5+/5+ years wet-lab and dry-lab experience, specializing in protein design and structural bioinformatics.
University of TokyoJapan
Pinned Repositories
AlphaCutter
This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.
awesome-protein-design
A curated list of awesome protein design research, software and resources.
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).
FPredX
This repository contains the FPredX models for the prediction of excitation maximum, emission maximum, brightness and oligomeric state of fluorescent proteins.
machine_discussion
Data and code used in the looped-ChatGPT-BARD "machine discussion" article.
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.
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
johnnytam100's Repositories
johnnytam100/AlphaCutter
This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.
johnnytam100/pdb2uniprot
A Python script to map PDB ID + chain ID to UniProt ID.
johnnytam100/awesome-protein-design
A curated list of awesome protein design research, software and resources.
johnnytam100/FPredX
This repository contains the FPredX models for the prediction of excitation maximum, emission maximum, brightness and oligomeric state of fluorescent proteins.
johnnytam100/NbX
This repository contains the NbX models for the re-ranking of nanobody–antigen binding poses.
johnnytam100/machine_discussion
Data and code used in the looped-ChatGPT-BARD "machine discussion" article.
johnnytam100/proteinsolver
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
johnnytam100/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.
johnnytam100/PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
johnnytam100/bio_embeddings
Get protein embeddings from protein sequences
johnnytam100/deep-protein-generation
johnnytam100/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).
johnnytam100/ibm3202
Google Colab Tutorials for IBM3202
johnnytam100/alphafold_20240830
Open source code for AlphaFold.
johnnytam100/esm_20240830
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
johnnytam100/evodiff_20240830
Generation of protein sequences and evolutionary alignments via discrete diffusion models
johnnytam100/install_AlphaFold2_on_GCP_VM
johnnytam100/making-it-rain
Cloud-based molecular simulations for everyone
johnnytam100/MD_learning
johnnytam100/preparemd
prepare AMBER files for MD simulations from a pdb file
johnnytam100/protein_generator_20240830
Joint sequence and structure generation with RoseTTAFold sequence space diffusion
johnnytam100/RFdiffusion_20240830
Code for running RFdiffusion
johnnytam100/trDesign
trRosetta for protein design