A curated collection of external resources, tutorials, and tools that we recommend for learning about computational chemistry, machine learning, bioinformatics, and chemical informatics.
Educational materials, courses, and tutorials to get you started
deep-learning-with-python-notebooks - Jupyter notebooks for the code samples of the book ‘Deep Learning with Python’
Getting-Started-with-Generative-AI - A curated list of articles and tutorials to start with and understand generative AI
awesome-generative-ai-guide - A one stop repository for generative AI research updates, interview resources, notebooks and much more!
ai4chem_course - The Artificial Intelligence (AI) for Chemistry course.
GNNs-For-Chemists - Implementations of different GNNs from scratch for chemists
DeepChem Tutorials - Machine learning for drug discovery tutorials
ML4MolEng Problem Sets - Problem sets for the MIT ML4MolEng course
dl-chem-101 - Deep learning for chemistry educational repository
AI4Chem - A course on AI for chemistry by the LIAC team at EPFL
Cheminformatics Material: Resources, Code, and Other things I use to teach Cheminformatics
Cheminformatics-Teaching-Material - Resources, Code, and Other things for Cheminformatics.
Awesome Python Chemistry - A curated list of Python packages related to chemistry.
Chemoinformatics-compiliation - Try to compile the sources of Cheminformatics that can be helpful for anyone that needs them.
Bioinformatics Material: Resources, Code, and Other things I use to teach Bioinformatics
awosome-bioinformatics - A curated list of resources for learning bioinformatics.
UC Davis Bioinformatics Core Training - UC Davis Bioinformatics Core Training Training course repository.
Structural-Bioinformatics - This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano.
Scikit-bio - A community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Materials for Drug Design and Discovery Computing Techniques
Awesome Drug Discovery - A meticulously curated resource list focused on computational methods for drug discovery.
TeachOpenCADD - A teaching platform for computer-aided drug design (CADD) using open source packages and data.
Open Source Molecular Modeling - Catalog of Open Source Molecular Modeling Projects.
AutoDock Vina - An open-source program for doing molecular docking.
DOCK - DOCK3 and DOCK6
rDock - A fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids.
Amber - Amber is a suite of biomolecular simulation programs.
GROMACS - A free and open-source software suite for high-performance molecular dynamics and output analysis.
OpenMM - A high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment.
MDAnalysis - A Python library for analyzing molecular dynamics (MD) simulations.
MDTraj - A python library that allows users to manipulate molecular dynamics (MD) trajectories.
Open-Source PyMOL - Open-source foundation of the user-sponsored PyMOL molecular visualization system.
UCSF Chimera - A program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments.
UCSF ChimeraX - UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
Regular updates and insights from experts
Greg Landrum’s RDKit Blog - Insights and tutorials on RDKit and cheminformatics
Pat Walters’ Practical Cheminformatics - Practical cheminformatics tutorials and insights
Is life worth living? - cheminformatics tutorials
Cheminformatics 2.0 - This blog is about chemical information software for next generation computing environments, broadly defined.
Practical Fragments - This blog is meant to allow Fragment-based Drug Design Practitioners to get together and discuss NON-CONFIDENTIAL issues regarding fragments.
Derek Lowe’s In the Pipeline - Commentary on drug discovery and pharmaceutical industry
Research Hub
AI4MolConformation - List of molecules ( small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning
GenAI4Mol - List of Molecular and Material design (molecular conformation generation) using Generative AI and Deep Learning
GenAI4Protein - List of papers about Protein Design using Deep Learning
AI for Chemical Spectra - Artificial intelligence and generative deep learning are used to unlock infrared spectroscopy(IR), mass spectroscopy spectroscopy, NMR spectroscopy, and chemical spectroscopy.
Interactive tools, utilities, and kits
Biopython - Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
CDPKit - The Chemical Data Processing Toolkit
MolPipeline - A Python package for processing molecules with RDKit in scikit-learn
scikit-mol - scikit-learn classes for molecular vectorization using RDKit.
mmpdb - A package to identify matched molecular pairs and use them to predict property changes.
mols2grid - An interactive molecule viewer for 2D structures, based on RDKit.
mordred - A molecular descriptor calculator.
ColabFold - Making protein folding accessible to all.
DockQ - A single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models.
reaction_utils - Utilities for working with datasets of chemical reactions, reaction templates and template extraction.
SMARTSPlus - Interactive SMARTS pattern matching tool
Open-source (AI-powered) software packages
RDKit - Open source toolkit for cheminformatics
Open Babel - Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Psi4 - Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python.
PySCF - Python module for quantum chemistry.
AlphaFold 2 - Open source code for AlphaFold 2.
AlphaFold 3 - AlphaFold 3 inference pipeline.
Boltz - Official repository for the Boltz biomolecular interaction models.
Open Chemistry - Permissively licensed cross-platform tools that provide applications for computational chemistry, materials science, and related areas.
Open Reaction Database (ORD) - Open-access schema and infrastructure for structuring and sharing organic reaction data
Comprehensive textbooks and reference materials
Machine Learning Glossary - This glossary defines artificial intelligence terms.
MIT Deep Learning Book - MIT Deep Learning Book in PDF format (complete and parts) by Ian Goodfellow, Yoshua Bengio and Aaron Courville.
Understanding Deep Learning - An authoritative, accessible, and up-to-date treatment of deep learning that strikes a pragmatic middle ground between theory and practice.
Deep Generative Modeling - Comprehensive book on models behind Generative AI
Andrew White’s Book - Deep Learning for Molecules and Materials
