PubChem peptide depictions: Part 2

Following on from my earlier post, I’ve been busy updating our Sugar’n’Splice peptide depictions to support some of the new features of our perception code, namely the presence of ester or thioamide linkages (instead of amide bonds), α-methyl groups, support for a greater range of N- and C-terminus capping groups, and support for bridges beyond disulfide (e.g. terminal Ac to Cysteine in one of the examples depicted below).

The following images, depicting structures from PubChem, illustrate some of these enhancements:PubChem Depictions 2

Substructure Search Face-off: Are the slowest queries the same between tools?

At the recent Cambridge Cheminformatics Network Meeting (CCNM) we presented a performance benchmark of substructure searching tools using the same queries, target dataset, and hardware. Whilst many tools publish figures for isolated benchmarks, the use of different query sets and variations in target database size makes it impossible to determine how tools compare to each other.

The talk compared the performance of various tools and offers insight in to the performance characteristics.

A question was asked at the talk as to whether the slowest queries were always the same. As expected there is some correlation (benzene is always bad) but there are some rather dramatic differences within and between tools. For example, the time taken to query Anthracene or Zinc varies with some tools finding Anthracene hits faster (marked as <) and others finding Zinc faster (marked as >).

The rank of slowest queries (per tool) is provided as a guide to how many queries took more time than listed here.

Anthracene Zinc
Tool Query Time (s) Rank (slow) Query Time (s) Rank (slow)
arthor 2.254 3 > 0.357 2602
arthor+fp 0.022 285 > 0.001 1667
rdcart 0.698 794 < 202 4
rdlucene 27.126 566 > 23.87 600
pgchem 28.231 138 > 18.181 197
mychem 48.289 108 > 34.145 159
fastsearch 396 99 > 285 126
bingo-nosql 0.448 451 < 1.311 260
bingo-pgsql 0.392 638 > 0.060 1228
tripod-ss 21.797 350 < 1441 18
orchem 27.075 906 > 0.721 2390

As promised the query and target ids are available: here.

If this is an area of interest to you feel free to get in touch.