Example 📓 Jupyter notebooks that demonstrate how to build, train, and deploy machine learning models using 🧠 Amazon SageMaker.

Having a pipeline for homology modelling using Modeller

Fast, accurate, and deterministic protein side-chain packing

Input files and analysis scripts for https://www.biorxiv.org/content/10.1101/2023.03.06.531337

Predicting housing prices from categorical and numerical data with gradient boosted regression trees.

An optimized version of alphafold 2 based on openfold

Exploratory PyMOL-MDAnalysis molecular visualization system.

Tutorials showcasing various capabilities of Libra

Semiempirical Extended Tight-Binding Program Package

Molecular Orbital PACkage

CREST - A program for the automated exploration of low-energy molecular chemical space.

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBFE) calculations on protein-ligand systems, compatible with …

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)

List of papers about Proteins Design using Deep Learning

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

Experiments with expanded ensembles to explore chemical space

Feature Generation Code

structures and data for https://doi.org/10.1039/D1SC03472C

binding free energy estimator 2

We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

Awesome papers related to generative molecular modeling and design.

AlphaFold2 non-docker setup

Modeling disordered protein interactions from biophysical principles

Code for running RFdiffusion

Constructing path-CV for advanced protein free energy simulations

Materials for the 2021 PRACE Workshop @ SurfSARA