Practical Cheminformatics - The Directory

In no particular order, here's a hopefully useful, topical organization of the posts I've written over the past few years.

Resources and Reviews

A Highly Opinionated List of Open Source Cheminformatics Resources

AI in Drug Discovery 2020 - A Highly Opinionated Literature Review


Viewing Clustered Chemical Structures in a Jupyter Notebook

Clustering 2.1 Million Compounds for $5 With a Little Help From Amazon & Facebook

Self-Organizing Maps - 90s Fad or Useful Tool? (Part 1)

Self-Organizing Maps - The Code (Part 2)

Molecule Generation

Automatic Analog Generation With Common R-group Replacements

Predictive Models

Predicting Aqueous Solubility - It's Harder Than It Looks

Assessing Interpretable Models

High-Performance Computing

Fast Parallel Cheminformatics Workflows With Dask

Wicked Fast Cheminformatics with NVIDIA RAPIDS


What Do Molecules That Look LIke This Tend To Do?

Adding Chemical Structures to a Recent COVID-19 Drug Repurposing Dataset

Filtering Chemical Libraries

Data Visualization / Plotting

A Collection of Things I Frequently Forget How To Do With Seaborn Scatterplots

Interactive Plots with Chemical Structures

Visualizing Chemical Space

Plotting Distributions

Molecular Modeling

Exploring the SARS-CoV-2 Main Protease (MPro) Structures

Building on the Fragments From the Diamond/XChem SARS-CoV-2 Main Protease (MPro) Fragment Screen (Part I)

Building on the Fragments From the Diamond/XChem SARS-CoV-2 Main Protease (MPro) Fragment Screen (Part II) Structure-Base Evaluation of Expanded Fragments

Assigning Bond Orders to PDB Ligands - The Easy Way

Scaffold Hopping? It's Complicated

SAR Analysis

Using the Structure-Activity Landscape Index (SALI) to Analyze Data From the SARS-CoV-2 MPro Screen

Examining the Data From the ChEMBL SARS-CoV-2 Drug Repurposing Screens

Positional Analogue Scanning

Using Reaction Transforms to Understand SAR

Free Wilson Analysis

A Few Updates to Free-Wilson

Model Evaluation / Statistics 

Some Thoughts on Comparing Classification Models

Benchmarking "One Molecular Fingerprint to Rule Them All"

How Good Could (Should) My Models Be?

Multiple Comparisons, Non-Parametric Statistics, and Post-Hoc Tests

Some Thoughts on Evaluating Predictive Models

Getting a Job

How to (Not) Get a Job in Science

How (Not) to Get a Job in Science - Part 2 - The Interview

Philosophical Musings

Where's the code?

Dissecting the Hype With Cheminformatics

AI in Drug Discovery - A Practical View From the Trenches

My Response to Peter Kenny's Comments on "AI in Drug Discovery - A Practical View From the Trenches"

Meeting Notes

Some Notes From the 2018 RDKit UGM

My Boring Life 

My Science/Programming Journey


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