Molecular Visualization

1. Molecular visualization: In the past several years, the software used to examine and display structure information has been greatly improved in terms of the quality of visualization and, more importantly, in terms of being able to relate sequence information to structure information.

   Visualization Tools:

   Although the RCSB Web site provides a Java-based three-dimensional applet for visualizing PDB data, the applet does not currently support the display of non-protein structures. For this and other reasons, the use of RasMol v2.7 is instead recommended for viewing structural data downloaded form RCSB; more information on RasMol appears in the following section. If a Java-based viewer is preferred, WebMol is recommended.

   The amino acid sequence in a given protein molecule determines the structure or the conformation of that particular protein. Protein conformation in turn determines the function of that particular protein. Hence, with the conformation or structure predicted, the function of any unknown protein can also be predicted with similarity search techniques. The relationship between sequence and function is primarily concerned with understanding the 3-D folding of proteins and inferring protein function from these 3-D structures.

   Molecular visualization helps the scientists to bioengineer the protein molecules. User-friendly graphic interface makes this area of Bioinformatics a full filled, scientific thrill to the bioscientists.

   Tools for molecular visualization:

   there are a number of software’s both free and commercial are available to visualize the biomolecules. The most commonly used free software are the RasMol, Chime, MolMol and Protein explorer and Kinemage Cn3D.

   1. RasMol

   most protein structure databases today come equipped with visualization tools, the most frequently used being the freely available RasMol (Sayle and Milner-White, 1995). The RasMol is derived from Raster (the arrary of pixels on a computer screen) and Molecules. This is a molecular graphics program intended to visualize proteins, nucleic acids and small molecules for which a 3-D structures is available. In order to display a molecular, RasMol requires an atomic co-ordinate file that specifies the position of every atom in the molecule through its 3-D Cartesian co-ordinates. rasMol accepts this co-ordinate file in a variety of formats, including the protein Data Bank (PDB) format. The visualization provides the user a choice of color schemes and molecular representation (wireframe, cylinder (Dreiding) stick bonds, alpha carbon trace, space filling (CPK) spheres, macro molecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface. Additional features such as test labeling for selected atoms, different colour schemes for different parts of the molecule, zoom, rotation, etc. have made this the most popular of all visualization tools.

   This standalone software can be downloaded from the RasMol homepage: www.umass.edu/microbio/rasmol

   RasMol and RasMol-Based Viewers

   As mentioned above, several viewers for examining PBD files are available. The most popular one is RasMol. RasMol represents a breakthrough in software-driven three-dimensional graphics, and its source code is a recommended study material for anyone interested in high-performance three-dimensional graphpics. RasMol treats PDB data with extreme caution and often recomputes information, making up for inconsistencies in the underlying database. It does not try to validate the chemical graph of sequences or structures encoded in PDB files. RasMol does not perform internally either dictionary-based standard residue validations or alignment of explicit and implicit sequences. RasMol 2.7.1 contains significant improvements that allow one to display information in correlated disorder ensembles and select different NMR models. It also is capable of reading mmCIF-formatted. Three-dimensional structure files and is thus the viewer of choice for such data. Other data elements encoded in PDB files, such as disulfide bonds, are recomputed based on rules of chemistry, rather than validated.

   RasMol contains many excellent output formats and can be used with the Molscript program to make wonderful postscript ribbon diagrams for publication. To make optimal use of RasMol, however, one mush master its command – line language, a familiar feature of many legacy three-dimensional structure programs.

   Several new programs are becoming available and are free for academic users. Based on RasMol’s software – driven three – dimensional – rendering algorithms and sparse PDB parser, these programs include Chime, a Netscape plug-in. Another program, WebMol, is a java – based three – dimensional structure viewer apparently based on RasMol-style rendering.

   
   2. Chime, protein explorer:

   chime and proteins explorer are derivatives of RasMol that allow visualization inside web browsers, while RasMol runs independently outside a web browser. Hence, it can be used only online, when connected to the Internet. Another feature of Chime is that, only certain molecules that are allowed by the company can be seen and not like RasMol where any protein molecule with atomic coordinates can be seen.

   Chime can be reached at: www.umass.edu/microbio/chime

   3. MMDB Viewer: Cn3D

   Cn3D is a three-dimensional structure viewer used for viewing MMDB data records. Because the chemical graph ambiguities in data in PDB entries have been removed to make MMDB data records and because all the bonding information is explicit, En3D has the luxury of being able to display three – dimensional database structures consistently, without the parsing, validation, and exception – handling overhead required of programs that read PDB files. Cn3D’s default image of a structure is more intelligently displayed.

   MolMol

   MoMol stands for Molecule analysis and Molecule display. This is also free software with a lot of features that are not found in RasMol and Chime. MolMol is a molecular graphics programme for display, analysis and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MolMol can be reached at: www.mol.biol.ethz.ch/wuthrich/software/molmol