ODDT: a sneak-preview screencast
Posted by Dr. Alex M. Clark in ODDT on 22-Feb-2012
To get a quick idea of how the Open Drug Discovery Teams (ODDT) project is coming along, check out this screencast. The ODDT app is at a fairly basic stage, but it is taking form nicely. Read the rest of this entry »
Mobile chemistry product roadmap
Posted by Dr. Alex M. Clark in cheminformatics, cloud-servers, mobile devices on 21-Feb-2012
With the American Chemical Society San Diego meeting coming up next month, and a year’s worth of new products and new features to cram into a 30 minute talk, now is as good a time as any to review some of the upandcoming developments that are on the roadmap for Molecular Materials Informatics.
These projects include some of the improvements that are intended for the near future. This planning ahead is just a snapshot in time, so entries will be added, deleted or reprioritised as necessary. Read the rest of this entry »
More about ODDT
Posted by Dr. Alex M. Clark in cheminformatics, mobile devices, ODDT on 14-Feb-2012
The previous post mentioned a new project in the works, called ODDT (short for Open Drug Discovery Teams, or anachronistically “Oddity”).
This is a project that was not even an idea 3 weeks ago when Sean Ekins started writing out some notes during a conference. In the interim time we got together and drew out a roadmap, built an app, put together some server infrastructure, and pitched the app in front of the Pistoia Dragon’s Den.
The project is currently immature, raw, and very far from finished – but this post covers some of the basics of what it is, and what it will grow into. Read the rest of this entry »
Working backwards: content creation, communication, consumption
Posted by Dr. Alex M. Clark in cheminformatics on 8-Feb-2012
The app ecosystem for mobile devices
has, for good reasons, been primarily oriented toward consumption of media content. This is particularly true of Apple’s touchscreen-only iPhones and iPads: these elegant portable computers make for a delightful way to peruse content, as evidenced by wildly popular apps like The Elements or Flipboard. Facile access to internet connectivity makes communication-oriented apps very effective, as witnessed by the number of mobile users of clients for social networks like Twitter and Facebook. Content creation, on the other hand, presents a significant challenge. Creating new data of any kind suffers from the inherent clumsiness of the finger-on-screen user interface paradigm, which makes something as simple as writing an email message somewhat of an inconvenience akin to learning how to touchtype all over again. Read the rest of this entry »
The unassailable value of cheminformatics
Posted by Dr. Alex M. Clark in cheminformatics on 6-Feb-2012
The overall field of computational chemistry/chemical information/computer assisted drug design can be divided up and categorised in any number of different ways, but one partitioning that seems particularly helpful to me is:
- using software to attempt to do real science
- using software as a glorified book-keeping toolset
The first category – real science – includes various kinds of efforts to model real systems, identify leads, predict properties, calculate binding affinity, etc. The second category – book-keeping – includes graphical presentation, data warehousing and relatively mundane operations, such as searching, performed on a large scale. Read the rest of this entry »
MolPrime+ released
Posted by Dr. Alex M. Clark in cheminformatics, mobile devices, molprime, property calculation on 4-Feb-2012
A few days ago, the MolPrime+ app passed through the AppStore filters and became available:
The “+” version provides all the features of the original MolPrime app, with an overhauled user interface, new cover art, updated sketching features, new property calculations, and no advertising… all for the price of $1. For more information, see the introductory article, or go straight to the AppStore.
Scientific publishing: is “open access” a disingenuous term?
Posted by Dr. Alex M. Clark in Uncategorized on 25-Jan-2012
Now is as good a time as any to put in my $0.02 worth on the scientific publishing industry. As someone who has needed to access journals while being inside the great academic library firewall, and outside of it, I have a well developed appreciation of the difference between the haves and the have-nots. As is obvious to anyone who has used the internet lately, the traditional business model of scientific journal publishers is functionally obsolete, since the most important value proposition – physically applying ink to paper and putting a postage stamp on the final product – is now an optional luxury that most readers could easily live without. Read the rest of this entry »
A new app is on the way: MolPrime+
Posted by Dr. Alex M. Clark in cheminformatics, MMDS, mobile devices, molprime, property calculation on 23-Jan-2012
There is now another iOS app waiting for initial approval on the AppStore, by the name of MolPrime+. As the name suggests, this is an enhanced version of the MolPrime app. Once the app gets through the review process, it will be available for the grand price of one dollar, whereas its predecessor was free. In return for this investment, advertisements are gone, some more advanced structure-properties can be calculated, and more graphics exporting options are available, including exporting vector graphics to Microsoft Word’s .docx format. And also the user interface has been overhauled, and if you’re not convinced already, it even has new cover art:
Dipping into ADME properties: log P and molar refractivity
Posted by Dr. Alex M. Clark in cheminformatics, cloud-servers, dropbox, molsync, property calculation on 12-Jan-2012
New functionality is being rolled out to the molsync.com server: a new implementation of log P and molar refractivity calculations, two important ADME properties. The functionality is currently available on the web-based interface:
SAR Table app: now with scaffold substructure searching
Posted by Dr. Alex M. Clark in cheminformatics, cloud-servers, mobile devices, molsync, SAR table on 10-Jan-2012
Version 1.1 of the SAR Table app just passed review and is available on the iTunes AppStore. This release is an important one, because it adds a major new feature: scaffold matching. For a row which has a whole molecule defined, and a scaffold core, the scaffold matching algorithm can be invoked to figure out the substituents:
