About

Not only computational molecular biologists or bioinformaticians use the Protein Data Bank PDB. Biologists, chemists, pharmacists, and many others can use it as well. If you are interested in a particular protein you may want to look up the basic information on your mobile Android phone. cmBot is an Android PDB client enabling you to get the look-up done in no time at all!

Motivation

Last summer I bought my first smartphone. It runs Google’s Linux-based operating system Android. When a professor told me that mobile computing didn’t have anything to do with bioinformatics, I asked myself “… or does it?”. Since then I wanted to apply mobile computing to topics from computational molecular biology. cmBot is my first shot at doing so.

Inside

The app consumes the PDB API. This means it looks up PDB ID’s and then parses the XML file the database returns in response. Finally, cmBot displays a nice overview of the file’s major facts - including a graphic visualization of the protein.

Target Group

Not only computational molecular biologists or bioinformaticians like me use the Protein Data Bank PDB. But also biologists, chemists, pharmacists, and all those who are somewhere in between. If you are interested in a particular protein and your PC or laptop is not available, you may want to look up the basic information on your mobile phone. cmBot makes this possible in no time at all!

Usage

When you start the app, your phone displays a search field with the default text “Enter PDB ID…”. It’s not quite difficult, you see… ;-) After entering the PDB identifier of your protein, which may be something like 2KTG for example, you submit it. Now the app connects to the PDB and retrieves the corresponding data, if the identifier exists. The app then prompts a structure image and a data sheet containing the following textual information:

tructure ID
itle
ubMed ID
eywords
umber of entities
umber of residues
umber of atoms
ublished on
eleased on
uthors
tatus

“Structure ID” and “PubMed ID” are displayed as links so the corresponding PDB and PubMed sites are just one click away.

Download & Installation

cmBot is not (yet) available from the Android app store, but you can install it following the instructions given below. There’s only one prerequisite: You need a smartphone running Android 2.2 or higher.

Download the archive from http://bioinformatik.o-dyn.de/cmbot/cmBot.apk to the SD card of your smartphone. Install it using one of the popular app installer apps (e.g. Easy Installer).

Contact

Feedback is strongly appreciated, so I can improve my app’s usability. Eva Kiszka (eva@o-dyn.de)