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Earlier posts considered exact matches to sequence representations in PubChem. Now, let’s look at what should be considered similar matches. It is a failing of structural fingerprints that (to a first approximation) all oligopeptides are similar to all...
The previous post introduced the concept of treating PubChem as a sequence database. In that post, structures with the same sequence were collated to search for alternative disulfide bridging patterns. Here we explore the general concept of using sequence identity...
While PubChem is best associated with small molecules, it contains an increasing amount of biopolymers through depositions of databases of molecules of biological interest (e.g. ChEBI, GuideToPharmacology) not to mention a large number of vendors. As every...

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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...
The example source code often provided with cheminformatics librariesto demonstrate the available functionality often try to address twoconflicting requirements. On the one hand, these attempt to bepedagogical teaching examples, explaining how to perform a...
Wikipedia is a highly useful source of Chemistry and also of chemical nomenclature. A limitation in chemical name to structure software, such as OPSIN, is that trivial names that are similar to systematic names may be misinterpreted if the program has never...

Latest posts linking here

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...
My cunning plan to get Roger Sayle to write down some of his findings has come to fruition. NextMove Software now has its own blog with posts from Daniel Lowe, myself and Roger on ChemSketch to Mol conversion, visualising a hierarchy of substructures, improving...