Several products are available from the Accelrys group for research in bioinformatics. Discovery studio (DS) products, which include MODELER, Ligand Fit, DS Visualizer etc., are very useful for computational biologists and bioinformaticists. For most practical applications, including rendering protein structure files obtained from the Protein Data Bank (PDB), DS Viewer 5.0 is very handy and comes with attractive options for the visual display of molecules. The vendors claim that you can “custom tailor the appearance of your model for maximum effectiveness,” and to a great extent, I find this to be true.
To begin with, DS Viewer can read a large number of input file formats including .pdb, viewer file, .xyz file, sketch files, and CSD files, to name a few. Additionally, new molecules can be generated from scratch by building in atoms of your choice and connecting them with bonds of the desired hybridization. Elemental properties can also be defined.
Pre-existing files can also be modified according to your needs. Groups can be added or removed and elemental charge, hybridization, stereochemistry etc. can be modified with ease using the atom add/remove/modify options. Torsion angles can be changed for either the backbone or side chain. However, the software does not warn if the torsion angles are, for example, disallowed, which should be kept in mind during modeling.
The software can carry out various calculations including torsion angles, distances, hydrogen bonds, etc. I use these options on a routine basis during the analysis of small molecule crystal structures and I find this software easier to handle than several others. Other calculations that can be performed include plane or centroid generation, exclusion volume calculation, VDW radius display etc. In the case of NMR structures, a single molecule can be quickly picked up when carrying out calculations. This molecule (or a part of the molecule) can be saved in a separate file for convenient analysis. Structures that do not have similar atoms can be superposed by tethering the sites. I find this feature especially handy, as several other software packages require similar atom numbers or atom types if a good superposition is to be obtained.
The display options of DS Viewer are also very good. Different display styles are available including ball-and-stick, CPK, line, ribbon etc.; each can be used for the entire molecule or for specific parts of the molecule. This is extremely useful for differentially highlighting specific residues in proteins. Additionally, stereo-visualization, 2D to 3D effect, and changing lighting effect can be carried out in just a few clicks. Animation tools are also available for generating movies of molecules in motion. The timeframe, rate of movement and the structures to be sampled can be defined during the animation. Simple rotation of the molecule along a specified axis can also be carried out. The generated images can be exported in several formats including Povray (for rendering images) or saved as .pdb, .xyz, or .msv files.
These are only a few of the features available in DS Viewer software (those that I commonly use). An overview of several other features can be obtained from the Accelrys website: http://www.accelrys.com/products/dstudio/viewerpro/. I must mention that like most other Accelrys products, this software is quite expensive. For those who only use rendering software for protein visualization and are not interested in the additional, interesting features of this software, there are free software packages which are available for download from various other websites. However, for those insisting on quality of images, this software is the best choice! You can download and install the trial version and buy it if you are satisfied.
Vikas Jain
Research Scholar
Indian Institute of Science
Molecular Biophysics Unit