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

Clustering

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


Databases


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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