The IUPAC International Chemical Indentifier (InChI) provides an open system for converting molecular representations into strings of text. Because text processing is one of the things computers do very well, InChI serves as an important link between chemistry and computer science. Unfortunately, the InChI documentation is rather scattered. To help remedy this problem, I have selected some links to Depth-First articles discussing InChI.
PubChem is arguably the most important free repository of information about small molecules on the planet. Although its size is staggering (over 10 million unique compounds), what makes PubChem important is its completely open approach to chemical information.
A recent article described how PubChem could be used to quickly search for CAS numbers. Although useful, the approach is limited in that only an array of PubChem CIDs was returned. What would be really useful would be a simple way to create a report with entries hyperlinked into the PubChem site itself to aid in visual inspection. In this tutorial, we’ll see how an HTML template and a few extra lines of code can do just that.
Recent D-F articles have discussed InChIMatic, a Web application that lets you search the Web for chemical structures by simply drawing them. InChIMatic takes advantage of InChI, a system for representing molecular structures as a strings of text, and Google, which indexes these text strings.
Synthetic Organic Chemistry has found a new pet. It’s called Organometallic Chemistry and comes in many breeds including the Piano Stool Sheppard, the Square-Planar Spaniel, and the ever-popular Metallocene Terrier. As much as Cheminformatics may want these unruly creatures to just go away, their intelligence and fierce, although easily-distracted, loyalty has earned a place in the hearts and notebooks of many chemists.
A very common operation in cheminformatics is the interconversion of molfiles and SMILES strings. Usually, converting from SMILES gives a molfile in which all atoms have coordinates of (0,0,0). Sometimes you just need more than that.
A D-F reader wrote in to ask how to calculate Topological Polar Surface Area (TPSA) using Ruby CDK. TPSA is one of the most widely-used descriptors for predicting membrane permeability and from it other important ADME properties. This article shows how to calculate TPSA with Ruby using Ruby CDK. The Library Our library consists of nothing more than a few method calls to manipulate the underlying CDK library.
Having spent a great deal of time with reCAPTCHA over the last few weeks, I’ve come to appreciate both the clever idea and spot-on execution. Aside from being an excellent product, reCAPTCHA also offers clues to building Web services that people will not just use, but also tell their friends about.
Slowly but surely, cheminformatics Web APIs are starting to appear. What’s the big deal, you may ask? By exposing Web APIs, service providers enable third parties to develop new applications that “mash up” functionality from two or more sites, or which take the original service in directions its founders never considered. By way of Antony Williams’ blog, I came across the announcement for the ChemSpider Web API.
