James Swetnam has an interesting article on security and the online chemical catalog. Apparently, the previous structure query results of a certain major retailer can be viewed by anyone, not just the person who originated them. Chemical structure queries, like any other database query, can be very valuable information in the hands of a knowledgeable and determined competitor.

Three-dimensional conformer generation is a common problem in cheminformatics. The most convenient and generally-useful method for creating chemical structures is the 2D chemical structure editor; applications that require three-dimensional representations need a way to generate reasonable coordinates from 2D user input. Until recently, there were no options for doing so with Open Source software.

A recent series of D-F articles have discussed the use of NestedVM to compile cheminformatics programs written in C/C++ to pure java binaries that can be run on any system with a JVM. More specifically, an attempt to compile OpenBabel’s babel program to bytecode was only partially successful. With the help of Geoff Hutchison, the problem was resolved.

Whether you’re a medicinal chemist or an informatician, QSAR datasets can be very helpful in understanding complex biological phenomena. These datasets typically consist of a hundred or fewer compounds associated with a specific parameter such as intestinal absorption, volume of distribution, blood-brain barrier penetration, or activity at one or more biological targets.

Chemistry World is running an article in its December issue titled Surfing Web2O that briefly touches on the subject of chemistry blogs. From analysis to commentary to news gathering, blogging is changing the way large numbers of people relate to each other and the world around them. Why should chemistry be immune to this phenomenon?

A recent series of articles discussed in some detail the process of compiling source code written in C and C++ to pure Java bytecode with NestedVM. But the full conversion process, starting with source and finishing with an executable jarfile, has to my knowledge never been documented.

Reference: Fukuzawa, Oki, Hosaka, Sugasawa, and Kikuchi, Org.