I had the pleasure of representing ARChem Route Designer, a retrosynthetic analysis tool from SimBioSys at the American Chemical Society meeting in Philadelphia last week. More…

Chem4Word Project from Microsoft and Murray-Rust

Following on from my presentation regarding text-mining and document mark-up at the ACS meeting in Philly it was interesting to see the announcement about the Chem4Word project from Microsoft. In collaboration with the Unilever School of Informatics at Cambridge university, and specifically working with Peter Murray-Rust and some of his team. From the website announcement it states:  “Microsoft Research is investigating the introduction of chemistry-related features in Microsoft Office Word, including authoring and semantic annotations. More…

Spaces, Dashes and Issues with Nomenclature Conversion

It appears that members of the text-mining for chemistry community are using one or more of the commercial name to structure software programs to convert chemical names to structures and, prior to feeding the algorithms, they are removing all white spaces from the names. They are also doing the same, in some cases, with dashes. How well is that going to work? Is it safe to remove spaces from chemical names and assume this has no effect? Is consideration being given more to the accuracy of the text-mining than to the nature of systematic nomenclature?

Let’s look at some examples of the result of removing spaces from chemical names. Consider the different results just from moving a space. READ MORE

Hamburger PDFs and Making Them Structure Searchable

This is just an fyi comment for the community really since this is a general assumption that Word Documents and PDFs cannot be made structure-searchable. The truth is that both can be made structure searchable. How? Well, you need to write the correct information into the file to enable it but it’s possible. There are a number of solutions out there allowing structure-based searching of Word document files. I believe the first one was originally from Oxford Molecular before being acquired by Accelrys. I think there are now multiple including, I believe, Cambridgesoft, ACD/Labs and probably others. READ MORE

A Green Solution for Virtual Screening Using the IBM Cell processor – An introduction to eHITS Lightning

FPGAs, GPUs and Cells – A Call for Comments from the Community

My New Found Friend for Microsoft Outlook – Meet XOBNI!