Waterfall plots are a common visualization method to view multiple spectra and have some similarities with joy plots. In the high throughput screening world, people have plot multiple dose response curves, offset on the z-axis to produce something that looks like a waterfall. An example is Figure 1 in Inglese et al, PNAS, 2006, 103(31). […]
Endnote XML to HTML or LaTeX
Over the last few years I’ve been maintaining my publication list as a BibTeX file, managed by BibDesk. This is handy when writing papers, but it’s also useful to use this data to keep my CV updated or generate a publications page. Since BibDesk can export to Endnote XML format, I put together a simple Python script to […]
Cryptography & Chemical Structure Search
Encryption of chemical information has not been a very common topic in cheminformatics. There was an ACS symposium in 2005 (summary) that had a number of presentations on the topic of “safe exchange” of chemical information – i.e., exchanging information on chemical structures without sharing the structures themselves. The common thread running through many presentations was to […]
Elemental Words
Last night, my colleague Matthew Hall tweeted Is there a app/site dictionary of all words possible with element symbols? #RealTimeChem — Matthew Hall (@cispt2) January 3, 2016 With the recent news of the 7th row of the periodic table being filled I figured this would be a good time to follow up on Matthews request […]
Maximally Bridging Rings (or, Doing What the Authors Should’ve Done)
Recently I came across a paper from Marth et al that described a method based on network analysis to support retrosynthetic planning, particularly for complex natural products. I’m no synthetic chemist so I can’t comment on the relevance or importance of the targets or the significance of the proposed approach to planning a synthetic route. […]