Open source ECFP/FCFP circular fingerprints in CDK

circular_rocAs of now, the latest version of the popular open source Chemical Development Kit (CDK) has its own implementation of the highly regarded ECFP and FCFP classes of chemical structure fingerprints (sometimes referred to as circular or Morgan fingerprints). While the general recipe for this kind of fingerprint has been available for awhile, and there are a number of implementations in various different toolkits, this one distinguishes itself in several ways: it has been implemented as closely as possible to the description of the original definition (without having access to the trade secrets that were left out of the paper); it includes resolution of chiral centres; it is freely available as open source Java code; and, last but not least, the algorithm is designed to be as portable as possible, with no major dependencies on specific programming languages or cheminformatics toolkits. Continue reading

Major new version of TB Mobile app

tbmobile2_intro1The TB Mobile app for iOS has just received a major new update on the iTunes AppStore. Version 2 of the app brings some fairly powerful cheminformatics functionality to this free mobile app for tuberculosis research. Produced by Collaborative Drug Discovery, built by Molecular Materials Informatics, and organised by Sean Ekins, this app is pushing the boundaries of real science on mobile devices in several important ways. Continue reading

MetaSearch options: and stealth OpenPHACTS prefilter

metasearch_optionsThe 1.5 release of the Mobile Molecular DataSheet (MMDS) introduced a couple of major features, including a minimum viable feature deployment of OpenPHACTS assay integration. That is being quite liberal with the meaning of viable: building this into a practical scientific workflow is more of an ongoing campaign than a specific new piece of functionality, and so other features are being improved in lock step. The next one to get an upgrade is the searching capability, which has an additional preflight configuration block (shown to the right). Continue reading

A rare word in defence of big pharma

If somebody were to start reading up on the exploits of current day pharmaceutical companies, one might get the impression that the industry got blindsided by calamities such as patent cliffs and the end of the blockbuster model, failed entirely to prepare for it, and lashed out incompetently in various disastrous, knee-jerk ways. But that’s not how it looked from my vantagepoint. Continue reading