Phylogenetic analysis in R

Data repository for distributing Amber force fields in the SMIRNOFF format

kinetic isotope effect prediction with Gaussian

Data and scripts to analyze netsci for paper.

User friendly and accurate binder design pipeline

Open source implementation of AlphaFold3

A Comprehensive Tool for Drug Property and Likeness Prediction.

Template-based protein design with Raygun

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

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

AlphaFlow Reinforcement Learning

PyMEMENTO

Python introduction for life scientists