User friendly and accurate binder design pipeline

This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user examples are also available.

A python module to plot secondary structure schemes

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Protein Ligand INteraction Dataset and Evaluation Resource

Code for running RFdiffusion

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Foldseek enables fast and sensitive comparisons of large structure sets.

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

High level API for using machine learning models in OpenMM simulations

Application to assign secondary structure to proteins

Helper for Bézier Curves, Triangles, and Higher Order Objects

A Python library for structural cheminformatics

Historical data on COVID-19 vaccination doses administered in Germany, per state.

A comprehensive macromolecular library

Visualization tool for changing networks

Source code and data for The Economist's covid-19 excess deaths tracker

Folding@home COVID-19 efforts

SVG path parser for matplotlib

Clustering by fast search and find of density peaks

A little word cloud generator in Python

Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

Jupyter widget to interactively view molecular structures and trajectories

A Python API for the RCSB Protein Data Bank (PDB)

IPython widget to interactively view molecular structures and trajectories

Simple library for reading trajectory coordinates

Tools for estimating and analyzing Markov state models

An open library for the analysis of molecular dynamics trajectories

Markov state model algorithms