bbyun28's repositories
DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
diffexpr
Porting DESeq2 into python via rpy2
DiffLinker
DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design
DiffSBDD
A Euclidean diffusion model for structure-based drug design.
FEgrow
An Open-Source Molecular Builder and Free Energy Preparation Workflow
foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
hignn
Code for "HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention"
machine-learning-notes
Collection of useful machine learning codes and snippets (originally intended for my personal use)
PEMT
Source code and data files for "PEMT: A patent enrichment tool with applicability in drug discovery"
Pocket2Mol
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
polyply_1.0
Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
practical-python
Practical Python Programming (course by @dabeaz)
python-mastery
Advanced Python Mastery (course by @dabeaz)
sanbomics_scripts
scripts and notebooks from sanbomics
ScaffoldGenerator
A CDK-based library for generating Scaffold Trees and Scaffold Networks
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
scvi-tools
Deep probabilistic analysis of single-cell omics data
StarGazer
StarGazer is a tool designed for rapidly assessing drug repositioning opportunities. It combines multi-source, multi-omics data with a novel target prioritization scoring system in an interactive Python-based Streamlit dashboard. StarGazer displays target prioritization scores for genes associated with 1844 phenotypic traits.
TankBind
Open source code for TankBind. Galixir Tenchnologies
TIES_MD
Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
Uni-GBSA
An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.