Computational biochemistry
- Rosetta and isopeptide bonds —How to model isopeptide bonds in Rosetta
- RDKit and PLP space
- Go away glycerol!! —Blacklist of ligands from crystallisation
- Lazy way to join protein and fill missing density
- PDB numbering rollercoaster
- Implicit waters and ligands in Rosetta
- Phosphorylated PDB files
- A note on the Linux PyMOL C01 atom oddity
- KEGG map colo(u)rs — KEGG maps accept hex triplet and an arbitrary set of color names.
Synthetic Biology
- What-if: Biosynthesis of deazaguanine —Nature does not make deazaguanine, but it would be very straightforward
- What-if: Metabolic engineering breaking bad — Some thoughts into how methamphetamine could be made by biocatalysis
- What-if: Lego's challenges for ABS biosynthesis — making the resin for Lego bricks by biocatalysis is really simple, but requires a lot of enzyme engineering
- What-if: unnatural amino acid biosynthesis — Some thoughts into how certain amino acids could be made.
- The non-green ocean — The oceans are pretty barren: how could nature overcome this?
Enzymology
- Speculations about methionine biosynthesis genes — Last year I published a review on the diversity of methionine biosynthesis . Here are some hypotheses and conjectures on the topic.
- The future of enzymology — perfect proteomics and metabolomics data and a hypothetical new version of metabolic modelling would render enzyme assays obsolete.
- Diaminopurine in cyanophage S-2L DNA — a cyanophage uses diaminopurine in its genome, a look into why this is not a synthetic biology buzzword.
- Fluorescent fats — conjugated ene bonds are fluorescent and some fluorescent fats are known, which would be an interesting synthetic biology reporter.
- The secondary metabolism of pineberry strawberries
- Pooled ORFome library by multiplex linear PCR — a sketch of an overly bold proposal that never was, combining GeneStrings and multiplex PCR to make a pooled ASKA-like library.
- Biochemical reaction yield and enzyme promiscuity — Reaction yield, a staple index with chemists, is feared in biochemistry.
- Promiscuously hitchhiking on a pathway — If one enzyme shows substrate ambiguity, chances are the next enzyme in the pathway show substrate ambiguity for that product, giving rise to shadow metabolism.
- GFP is a suicide enzyme —Ehm?!
Microbiology
- Pseudomonas, Ralstonia and Burkholderia: HGT buddies — these three genera belong to different orders, but were once mistaken the same genus. It turns out they have shared a lot of genes, which raises the hypothesis that cause the early categorisation.
- Bacterial dissociated press — I wrote a script to make up bacterial names by Markov chain, this is what I got.
Coding
- Convert Python docstrings to GitHub markdown readmes
- Pictograms with Plotly and FontAwesome
- A better progressbar for Jupyter notebooks
- Python website on a shoestring (on a pi at home)
- Uniprot XML and Python ElementTree or alternatively via a dictionary
- PDB in Office 365
- Exporting Jupyter notebooks with Plotly graphs
- A failsafe decorator for a python class
- Pythonic spinner — Ever want to proudly show the world that your server runs Python? Here is a spinner icon just for the trick (Get it from the spinner's GitHub repository )
- A simple arrow between bootstrap cards
- Toasty CSS with BS4
Other
- Life expectancy in Middle-Earth: elves and mortality tables — Elves only die of external causes, which should follow a geometric distribution, which lets us see that the US is more dangerous than Middle Earth.
- Vulcan birthday calculator — How many Vulcan years old am I?
- Wikipedia datamining
- When will the PDB run out of 4-letter codes?
- Medical diagnostics with mutazyme? — The most ridiculous disclaimer is that Mutazyme cannot be used diagnostically. So ridiculous there must be a conspiracy.
- Homologues and synonyms — comparison of words and genes, and how Thermotoga and English are rather alike.
- Publication-driven complexification — if a method works it will get cited. To get a slice of that citation action the done thing is to publish an even more complicated method. This arms race results in excessive mathemagic, maths so complicated, it is the same as magic.
- Thesis word cloud — a word cloud of my PhD thesis
- Nature's profits — $34 per article is a rip off as is the whole journal publishing industry
- NZSBMB conference report — A conference report I wrote for the NZSBMB newsletter
- A map of Britain through a kaleidoscope — a cool idea for predictions of where missing town names are in former British colonies
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