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Following on from the work described in the last post, I have put together a dataset of text-mined peptides which I’ve uploaded to PubChem. This involved extending our biopolymer grammar (which I use to textmine with LeadMine) and improving the ability...
As part of my work on Sugar&Splice, I regularly search through PubChem for biopolymers where we recognise most of the components, but maybe miss one or two. My typical approach is to extract the SMILES strings of these monomers, and consider the most commonly...
Roger, John and I will all be presenting talks at the upcoming 256th ACS National Meeting in Boston. There’s also a related talk by the folks at Chemspace about their integration of Arthor for substructure and similarity search. As an addition to the...

Most popular posts

CC[C@](CO)([H])[14CH2]CThe CIP (Cahn-Ingold-Prelog) priority rules are used to assign R and S labels to stereocentres. However it is known to be very prone to mis-implementation:The CIP System Again:? Respecting Hierarchies Is Always a MustThrough our work...
I attended the ever-excellent Sheffield Cheminformatics – sorry – Chemoinformatics Conference last week where I presented a poster on Sugar & Splice, Macromolecules or Big Small-Molecules? Handling Biopolymers in a Chemical Registry System...
In an earlier post, I described a simple procedure to generate a hierarchy of substructures, and depicted the hierarchy with GraphViz. Pat Walters at Vertex realised that it is possible to add images as node labels in GraphViz and updated the script so that...

Latest posts linking here

I'm please to announce that my PhD thesis is now available from the Cambridge DSpace repository: https://www.repository.cam.ac.uk/handle/1810/246652. One thing potentially of note is the description of fast Kekulisation that I originally intended to write as...
Conferences are all about communication. But what can and cannot be communicated at a conference, or rather what should and should not? Probably top of the list of "should not" is to use inappropriate examples or images to liven up proceedings. Recently I attended...
Because of the relationship between SMILES and SMARTS, there are some fun tricks you can do (for some value of fun). For example, over at the NextMove blog I have written about creating a substructure hierarchy (here and here). Here's another example I came...