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The Bumbling Biochemist

The Bumbling Biochemist

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Author: Brianna Bibel

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Make the switch to extended PDB IDs and PDBx/mmCIF files – what, why, how

May 12, 2025January 6, 2026

As the PDB (Protein Data Bank) grows, it is running out of 4-character PDB IDs (accession codes you use to […]

The DPC assay for measuring Cr(VI)

April 29, 2025April 29, 2025

The main reason the heavy metal chromium is so toxic is that it’s an oxidant. The hexavalent form of Cr, […]

Resources and recommendations for generating & working with protein alignments

April 23, 2025July 23, 2026

Derivatization of metabolites for GC-MS via methoximation+silylation

March 9, 2025July 6, 2025

Silylation may sound silly to say, but if you want to make organic acids volatile for GC-MS, it gives you […]

Experimental planning spreadsheets

February 22, 2025May 27, 2025

 

The many “colors” of chromatography, especially TLC

February 10, 2025February 25, 2025

Chromatography literally means “writing in color” because it was originally used to separate colored pigments. Nowadays, chromatography has a number […]

Exciting career update!

January 30, 2025January 31, 2025

Signed! It’s official – I am incredibly excited to announce that I have accepted a tenure-track Assistant Professor of Chemistry […]

Reasonableness checks

January 29, 2025January 29, 2025

Before you use your calculator (or even your pencil), use your brain! Silly errors are easy to make when doing […]

Nucleophilic acyl substitutions – swapping what’s hooked up to carbonyl C’s

January 10, 2025April 28, 2025

In nucleophilic acyl substitutions you swap out what’s attached to a carbonyl carbon Because oxygen is more electronegative (electron-hogging) than […]

Cool carbonyl chemistry

January 8, 2025November 22, 2025

Much of biochemistry is carbonyl chemistry – so here’s some more about some of why this is and what to call […]

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