Multiple Protein Structure Alignment at Scale with FoldMason

Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.

Protein Ligand INteraction Dataset and Evaluation Resource

A short course on proteins and protein design aimed at early career students

ShuffleAnalyzer is a python-based tool for the analysis of DNA-shuffling and peptide insertions in synthetic biology.

Cross-platform software to draw phylogenetic trees

In silico directed evolution of peptide binders with AlphaFold

PoreAnalyser is package written by @DSeiferth that expands HOLE results to consider asymmetry and estimate conductance

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.

Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces

Analysis of non-covalent interactions in MD trajectories

List of papers about Proteins Design using Deep Learning

A collection of resources and papers on Diffusion Models

This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua

Rifdock Library for Conformational Search

AlphaFlow Reinforcement Learning

PyMEMENTO

Python introduction for life scientists

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling

Constructing path-CV for advanced protein free energy simulations

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

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

Analysis tool for GetContact Frequencies