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Lectures

Free lectures for anyone who has taken Organic Chemistry I & II and a data-structures course.

Level
Format
Topic

Undergraduate Cheminformatics

001Undergraduate · Article

How to Write SMILES: Converting Skeletal Diagrams to 1-D Strings

SMILES
002Undergraduate · Article

Expanding SMILES to Alkenes, Alkynes and Carbonyls

SMILES
003Undergraduate · Article

String Formation Algorithms & Canonical SMILES with RDKit

SMILESRDKit
004Undergraduate · Article

Virtual Atoms and Bonds for Combinatorial Libraries

SMILES
005Undergraduate · Article

Chemical Data Formats and Writing Your Own Mol2 Parser

SMILES
006Undergraduate · Article

Stereochemistry in SMILES with RDKit

SMILESRDKit
SpecialUndergraduate · Article

Introduction to Cheminformatic Law

Law and Compliance

Graduate Cheminformatics

001Graduate · Article

Your 1st Million SMILES

SMILES
002Graduate · Article

Exploring the Chemical Universe with Potential Energy Functions

Force Fields
003Graduate · Article

Approaching Machine Learning as an Organic Chemist

Machine Learning
004Graduate · Article

Building Your First Cheminformatic Bot with Discord and GitHub Actions

RDKit

Video lectures

V1Undergraduate · Video

Introduction to SMILES 001: Alkanes & Alcohols

SMILES
V2Undergraduate · Video

Introduction to RDKit 001: Molecule Properties

RDKit
V3Undergraduate · Video

Introduction to RDKit 002: Analyzing Cannabis Molecule Property Distributions

RDKit
V4Undergraduate · Video

Jupyter Notebook for Scientists

Machine Learning
V5Undergraduate · Video

Putting Molecular Dynamics Simulations in a Presentation

Molecular Dynamics

Machine learning

ML1Graduate · Notebook

RNN to Convert IUPAC to SMILES

Machine LearningSMILES
ML2Graduate · Notebook

Probability Density of Any Set of Numbers

Machine Learning
ML3Graduate · Notebook

Graph Networks for IUPAC Nomenclature and SMILES

Machine LearningSMILES
ML4Graduate · Notebook

Decoding Fingerprints to Chemical Names

Machine Learning
ML5Graduate · Notebook

Levenshtein Distance on IUPAC Names for NLP

Machine Learning
ML6Graduate · Notebook

Connecting Global-Chem to a Neo4j Graph Database

Knowledge Graphs
ML7Graduate · Notebook

Designing a Convolutional Neural Network for Cannabis Machine Learning

Machine Learning
ML8Graduate · Notebook

Statistics Teaching Material

Machine Learning

Force fields and molecular dynamics

FF1Graduate · Article

What Are Force Fields? A Coder's Perspective into CHARMM

Force Fields
FF2Graduate · Article

Understanding Atom Types: The Philosophy

Force Fields
FF3Graduate · Article

Checking Simulation Log Files with Python

Molecular Dynamics
FF4Graduate · Article

Controlling Tumbling Effects in MD

Molecular Dynamics
FF5Graduate · Article

How I Check for Convergence in My Simulations

Molecular Dynamics

Combustion

C1Graduate · Article

Laminar Flame Speed

Combustion

Full curriculum · 111 items

Everything in the teaching repository

Every article, video and notebook, organized by subject. The search box above filters this list too.

01Lecture Series

  1. How to Write SMILES: Introduction to Converting Skeletal Diagrams to 1-D Data String Representation.
  2. Expanding SMILES to more Diverse Functional Groups: Introduction to Alkenes, Alkynes, and Carbonyls.
  3. Designing String Formation Algorithms & Introduction to Canonical SMILES with RDKit
  4. Manipulating SMILES strings with Virtual Atoms and Bonds to create Combinatorial Libraries.
  5. Understanding Chemical Data Formats and Writing Your Own Mol2 Parser Part 1.
  6. Introduction to Stereochemistry in SMILES with RDKit
  7. Introduction to Cheminformatic Law
  8. Your 1st Million SMILES
  9. Exploring The Chemical Universe with Potential Energy Functions.
  10. Approaching Machine Learning as an Organic Chemist Part 1
  11. Building your First Cheminformatic Bots with Discord And Github Actions.
  12. Alkanes & Alcohols
  13. Molecule Properties
  14. Analyzing Cannabis and Taking the Probability Distribution of Molecule Properties
  15. Setup Port Forwarding, And Managing Imports
  16. Putting Molecular Dynamics Simulations in a Presentation

02Organic Chemistry Standard Mechanisms

  1. Hydrobromination of Styrene in SMILES
  2. Friedel-Crafts Alkylation in SMILES
  3. Diers-Alder Reaction in SMILES
  4. Diers-Alder Reaction of Bicyclo Compounds in SMILES

03Development Operations

  1. A Comprehensive Overview for releasing a Python Package for Scientific Publication.
  2. Using Python Glances to Monitor Your System
  3. Modern Github Badges For Open Source Repositories
  4. Automating Cheminformatics with Apache Airflow — Step 1: Preparing SMILES Transformations on Large Scale
  5. Downloading the Zinc Database Rapidly with Aria2
  6. Useful Github Actions Bots to Regulate my Python Package
  7. Debugging File Encoding and File Path Distribution Bugs for GlobalChem with Github Action Bots.
  8. Using Psi4 on a High Performance Cluster
  9. Designing an Interoperable Chemical Knowledge Graph
  10. Managing Open Source Licenses For Python Package Dependencies
  11. Python Design Documentation Part I: Goodbye ReadTheDocs, Hello GitBook
  12. Distributing Python Main and Submodules on PyPi

04Principal Component Analysis

  1. Principal Component Analysis on the list of SMILES from Pihkal using GlobalChem and IUPAC
  2. Using Principal Component Analysis to distinct Aromatic and Non-Aromatic Compounds and Identify Common Scaffolds for Diverse Communities using SMILES and Global
  3. Understanding what is inside of Cannabis Sativa using Principal Component Analysis with Global-Chem
  4. Mixing Global-Chem Nodes: Cannabis Sativa and Oral Contraceptives for Principal Component Analysis.
  5. Principal Component Analysis on Alternative Jet Fuels with Global-Chem

05Cheminformatics

  1. Understanding drug-likeness filters with RDKit and exploring the WITHDRAWN database.
  2. Preparing Chemical Data in 5 minutes with Cocktail Shaker, RDKit, and Pandas
  3. Trends in fingerprint matching of peptides using Tanimoto, RDKit, and Cocktail Shaker.
  4. Converting a List of SMILES to PDF form.
  5. Understanding Morgan and converting the chemical structure to a number.
  6. Using the MiniFrag Database to validate your SMARTS strings
  7. Validating SMILES with RDKit, PySMILES, MolVS, and PartialSMILES
  8. Protonating your SMILES strings over a range of pH for Small Molecules and Proteins
  9. Using Modin or GPU to read in massive datasets of molecules.
  10. Exploring Promiscuous Tetrahydrocannabinol (THC) Chemical Space
  11. Sn1, Sn2, E1, E2 Mechanism Explained in SMILES.
  12. Aziridine
  13. Selection of Functional Groups for Chemical Nerve Toxic Agents — Novichok
  14. Overriding Gasteiger Partial Charges in RDKit
  15. Probability Distribution of Chemical Fingerprint Similarity Scores with RDKit and Plotly.
  16. Bostrom’s Algorithm in Python For Protein-Ligand Binding.
  17. Part 1 — Connecting GlobalChem Knowledge Graph to Neo4j Graph Database
  18. Part 2 — Querying Common Chemicals with ChatGPT From a Neo4j Database
  19. Principles of Chemical Diversity
  20. Converting your Knowledge Graph TSV/CSV to a Resource Description Framework (RDF) For Interoperability
  21. Partial Charged Fingerprints
  22. Uploading Structured Chemical Data to Wikidata
  23. Chemical Composition of Holy Water
  24. Converting a List of IUPAC names to SMILES
  25. Retrosynthesis Artificial Intelligence
  26. Looking at the Chemicals Inside Sephora Makeup Foundations For Any Toxic Alerts
  27. Converting an Image of a Molecule to SMILES
  28. Exploring Chemical Space: Insect Sex Pheromones
  29. Convert a list of CAS numbers to SMILES using Pubmed, Cirpy, or a Recurrent Neural Network

06Medicinal Chemistry

  1. Designing a Good Injectable Drug

07Computational Chemistry

  1. Symmetry-Adapted Perturbation Theory (SAPT) of Helium in Psi4
  2. Harmonic Analysis in Psi4
  3. Optimizing A Molecule’s Geometry with Psi4
  4. Visualizing Frontier Orbitals with Psi4 and Python
  5. Your First Lennard-Jones Potential Energy Scan

08Molecular Dynamics

  1. Converting GRO files to PDB using Python
  2. Calculating the End-to-End distance of two atoms using MDAnalysis
  3. Using python to check molecular dynamic simulation log files.
  4. How I was checking to tell if there was convergence in my simulations.
  5. Controlling Tumbling Effects in a Molecular Dynamics Simulation.
  6. Analyzing Dipole Moments in Molecular Dynamics Simulations
  7. Exploring Multi-Processing for Exhaustive Hydrogen Bonding Analysis using MDAnalysis and Futures
  8. Calculating Density of a Neat Liquid from a Molecular Dynamics Simulation with NAMD
  9. Maintaining Constant Pressure and Temperature in NAMD.
  10. Part 1 Molecular Dynamics: Simulating Kinases using CHARMM and Amber
  11. Part 2 Molecular Dynamics: Retaining Water in the Crystal Structure.
  12. Running Molecular Dynamic Simulations on Github Actions with GROMACS
  13. A Hugging Face Chat assistant to tell us what are the chemicals inside of Cannabis Sativa

09Machine Learning

  1. Exploring bridging cheminformatic languages between machines and humans using AI — Part 1
  2. How to take the probability density of any set of numbers and make an analysis.
  3. Exploring Graph Networks for IUPAC Nomenclature and SMILES.
  4. Using IUPAC with GlobalChem Sunbursts to determine Chemical Diversity for a list of SMILES with Plotly.
  5. Sunbursting the FDA Colour Additive 7 Lists through ToxAlerts.
  6. Decoding Fingerprints to IUPAC/Natural Chemical Names
  7. Applying Levenshtein distance on IUPAC/Preferred names in GlobalChem for Natural Language Processing.
  8. A Newick Tree for Protein Families and Relations
  9. Part 1 — Connecting GlobalChem Knowledge Graph to Neo4j Graph Database
  10. Designing a Convolutional Neural Network For Cannabis Machine Learning Part 1
  11. An Assignment For Optimizing Non-Linear Functions to Machine Learning Students
  12. Combining Chemical Languages with ChatGPT using Large Language Models (LLMs) Part 1
  13. Resurrecting the Dead: Alexander Shulgin Large Language Model Agent with Langchain
  14. Using Chat-GPT and Freedom of Information Act to Gather Imports/Exports of Drug Seizure Data
  15. Converting Your Knowledge Graph CSV into a Large Language Model With Langchain and ChainLit.

10Force Fields

  1. What are force fields? A coder perspective into CHARMM.
  2. How to take the probability density of any set of numbers and make an analysis.
  3. Inclusion of Atom Types in Force Fields to produce mixed CXSMILES, CXSMARTS, CurlySMILES
  4. Mixing CGenFF Atom Types to RDKit Mol2SVG Function and Visualizing

11Combustion Mechanics

  1. Laminar Flame Speed

12CHARMM Errors

  1. Charmm Error: Warning from RDCMND, Command Line Too Long.
  2. Charmm Error: Energy Change Tolerance Exceeded

13Compliance

  1. Making Global-Chem Github Repository 21 CFR Part 11 and FAIR compliant for U.S and European Countries.
  2. Ethical Artificial Intelligence Data Sharing Clauses For B2B Agreements

14Miscellaenous Resources

  1. How to Host Static Websites for Cheap.
  2. Implementing Github Code spaces for an Academic Lab.
Full curriculum on GitHub →