IntelliFold: A Controllable Foundation Model for General and Specialized Biomolecular Structure Prediction.

Protein-RNA binding affinity 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

parallel fastq-dump wrapper

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

Computational Chemistry Workflows

A Python frontend to the LigPlot+ program, allowing batch processing of Protein Data Bank (PDB) files through the DIMPLOT algorithm.

For ligand-binding residues prediction

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.

Loop Modeling in protein structures

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily