by July 4, 2002 0 comments



One of the reasons for the accelerated pace in biomedical research is the availability of software to aid the complex computations required. There’s software to store, retrieve, analyze and predict the composition or the structure of biomolecules. They can translate the structure of a molecule into one that can be replicated, dissected into individual parts and given visual 3-D form. 

Here we look at one bioinformatics software, called Protein Explorer, which is meant to explore macromolecule structures in 3D. It is operated through a Web browser and can show structures of proteins, DNA, RNA, carbohydrates or even enzymes and drugs. To begin using it, you need to download a browser plug-in called Chime from
www.umass.edu/microbio/chime. It runs on Netscape and IE. After installing it, open a browser window and go to
www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/. Here click on the link Quick-Start Protein Explorer.

Protein explorer shows the structure of proteins, DNA, enzymes and even drugsThe Protein Explorer browser interface is split into four panes. The window on the right contains a 3D macromolecule. The structural data for this molecule comes from a Protein Data Bank and obtained either through X-Ray crystallography, solution nuclear magnetic resonance or theoretical modeling. For you to view molecules, it is important that you know their four letter Protein Data Bank ID. All published macromolecule structures have such an ID. You can search for particular molecules in the protein data banks as well. The default molecule loaded in your screen is 1D66.pdb, which is called a zinc-finger protein.

One of the goals of Protein Explorer is for novices to be able to concentrate on the molecular structure available to them, and not on the software required to see it. This is a key factor that bioinformatians need to keep in mind when designing these tools. In Protein Explorer, you can view a molecule from any angle by holding your mouse key down on and turning it around. You can change the rendering to better highlight certain parts of the molecules. You can render it based on different variables to better present your understanding. Display options for the molecule range from displaying hydrogen bonds or disulfide bridges (among others) to dot surface displays, shadows, labels, sprouted Hydrogen and stereo display. 

The upper left frame of Protein Explorer is the driver’s seat to get to all information about the molecule. From here, you can control various display options, like spinning, hiding water molecules, etc. It can split into two frames and provide information and helpful tips in a child frame. There are links on this window that lead you to other resources like the Protein Data Bank. There’s another tool in Protein explorer that downloads specific molecules to your hard disk.

The lower and third frame of Protein Explorer are message boxes containing information about the atoms you click on. It also enables experts to type in commands in chime script. Here you can also generate distances between atoms, angles, dihedral angles and attach arbitrary labels to atoms. You can also right click on the molecule in the right pane and view it in various forms. 

Priya Ramachandra

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