In the September 2010 BioTechiques editorial, we surveyed a handful of applications designed with the bench scientist in mind.
In the "iPad Apps for Scientists" article series, we expand upon that collection to include useful iPad and iPhone applications for life scientists.
We encourage you to join in the discussion by sharing your favorite apps in the Molecular Biology Forums.
Other "iPad Apps for Scientsist" articles: Fluorescent imaging | Scientific calculators | Taking PubMed to the next level | Proteins on display
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The number of available protein structures is rapidly growing as scientists deposit their resolved structures into databases on a daily basis. In the past, to visualize one of these structures, researchers would have to first download a structural dataset for a particular protein and then import that file into a specialized software program capable of rendering the structure, a process that required both time and knowledge of the numerous protein and DNA databases available.
But new mobile apps are shortening the time needed to find and render a structure, providing more information to researchers than previously imaginable in a mobile format. Here we look at two new protein apps available for the iPad; these work together to make finding a protein of interest and it’s structural information as easy as snapping, or tapping, your fingers.
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iProtein
While the home screen for iProtein appears clunky and lackluster at first glance, don’t let the looks deceive you—what lies underneath is most certain to keep those working on proteins coming back. There are five possible areas to click on the homepage: sequence, structure, families, sites, and bound ligands. The sequences and structures options allow you to enter a single searchable keyword or a PDB code which will generate a list of all proteins matching your input query, either in an amino acid or structural format. In the sequence mode, a tap on the downloaded sequence will initiate a sequence search to recover similar sequences, while structure mode generates a list of the protein title, classification, sources, resolution, reference and, of course, the structure itself. In families, you can explore the various members of different protein families, again from both a structural and sequence perspective.
The final option—bound ligand—can be interesting for both the medicinal chemist and the budding artist. The interface allows one to build their own molecule and then submit their designed structure for potential protein interactions. If your ligand has been shown to bind a protein, the app provides a list of the ligand hits, PDB information, and the particular site where the ligand binds. To visualize ligands, as well as protein structures, iProtein links out to another impressive iPad protein app called Molecules.
Name: iProtein (iTunes)
Price: $4.99, 5-day free trial
Platform: iPad
Manufacturer: Eidogen-Sertanty, Inc.
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Molecules
A nice addition would be the ability to identify key amino acid residues in a particular structure or focus on only a section of a specific protein. While these features would make the usability of Molecules even greater for scientists, this version does provide a way to explore the expansive universe of proteins quickly, from virtually anywhere.
Name: Molecules (iTunes)
Price: Free
Platform: iPad, iPhone
Manufacturer: Sunset Lake Software
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We encourage you to join in the discussion by sharing your favorite apps in the Molecular Biology Forums.
Other "iPad Apps for Scientsist" articles: Fluorescent imaging | Scientific calculators | Taking PubMed to the next level | Proteins on display
