UENO M.'s starred repositories
alphafold3-pytorch
Implementation of Alphafold 3 in Pytorch
se3-transformer-public
code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503
PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
rf_diffusion_all_atom
Public RFDiffusionAA repo
se3-transformer-pytorch
Implementation of SE3-Transformers for Equivariant Self-Attention, in Pytorch. This specific repository is geared towards integration with eventual Alphafold2 replication.
alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
Illustrate
Biomolecular Illustration Tool
gpusimilarity
A Cuda/Thrust implementation of fingerprint similarity searching
zsh-jupyter-kernel
Z shell kernel for Jupyter Notebook
AF_unmasked
Source code and examples for AlphaFold Unmasked
binana
BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding. It is useful because accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study. We have also created a BINANA web-browser application.
pyrosetta_scripts
A place in which scripts developed in PyRosetta can be stored and shared. In the not too distant future, these scripts will be tested along side the main repository to ensure that they continue to work even if we make changes to the interfaces of core classes.