Starred repositories
IntelliFold: A Controllable Foundation Model for General and Specialized Biomolecular Structure Prediction.
Scripts for accelerating your Bioinformatic data processing
All UCSC Genome Browser source code that is under an open source license, mostly file format converters, command line tools and C libraries. A subset of the "kent" repo, updated every three weeks.
Interactive data analysis and visualisation with chemical intelligence
The Rosetta Bio-macromolecule modeling package. Available through license with the University of Washington.
Toolkit for linearizing PDFs for LLM datasets/training
R package to compute dissimilarity between multivariate time series
#1 PDF Application on GitHub that lets you edit PDFs on any device anywhere
Graphic notes on Gilbert Strang's "Linear Algebra for Everyone"
Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.
Fast computation of Distance Correlation and Distance Covariance in R
Contacts-based classifier of biological and crystallographic interfaces
RAD Lab enables users to deploy infrastructure on Google Cloud Platform (GCP) to support specific use cases. Infrastructure is created and managed through Terraform in conjunction with support scri…
Run AlphaFold2 (and multimer) step by step
Auto3D generates low-energy conformers from SMILES/SDF
DrugGPT: A GPT-based Strategy for Designing Potential Ligands Targeting Specific Proteins
A Python frontend to the LigPlot+ program, allowing batch processing of Protein Data Bank (PDB) files through the DIMPLOT algorithm.
Providing six different algorithms that can be used to split the available data into training, test and validation subsets with similar distribution for hydrological model developments.
Spatiotemporal identification of druggable binding sites using deep learning
ProteinGCN: Protein model quality assessment using Graph Convolutional Networks
BPL is an Python app to solve Loop Closure Problems.
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily