J.

Atoms and Molecules/ 3(5); 2013 / 576578 Review article

Barik BP

Journal of Atoms and Molecules

An International Online Journal
ISSN 2277 1247

COMPUTATIONAL VISUALIZATION OF BIOMOLECULAR STRUCTURES Bibhuti P. Barik Post Graduate Dept. of Bioinformatics, North Orissa University, Sriramchandra Vihar, Takatpur, Baripada, Odisha, India, PIN- 757003. Received on: 05-09-2013 Revised on: 19-09-2013 Accepted on: 28092013 Molecules constitute a cells complex internal structures in the living organisms. The biological macromolecules form 3D structures from their primary sequence of linear chain of molecules. Each has its characteristic sequence of subunits, its unique three dimensional structures, and its highly specific selection of binding partners in the cell. The structure of any biological macromolecule imparts functions to the macromolecules and thus allows better understanding of the structure function relationship. Visualization is the process of interpreting visual images of biomolecules. It is the process of creating visual representations of biomolecules and qualitatively interpreting their meaning. These representations allow investigators to model specific features of a molecule. Literally visualization is much more complex than simply viewing molecular images. Molecular viewing is to just view the structure rather extracting chemical information from it. Interpretation is more difficult in case of molecular viewing. Tools are required to perform comparative analytical studies of biomolecular structures predominantly nucleic acids, proteins and different chemical * Corresponding author Bibhuti P. Barik, Email: bibhutiprasadbarik@gmail.com Tel: +91 9937410360 All rights reserved 2011 structural families. Viewing and studying the 3D structure helps in different ways. Visualization studies may help in determining the overall shape and size of molecules, locating a residue of interest in the overall structure, locating a residue of close proximity to a residue of interest, developing or testing chemical hypotheses regarding an enzyme action, locating or predicting binding sites of a ligand and to interpret mutation studies, finding the areas of positive or negative charge on a protein surface, locating particularly hydrophobic, hydrophilic region of a protein, studying evolutionary processes at the level of a molecular structure, inferring the 3D structure and related properties of a protein with unknown structure from the structure of a homologous protein. Moreover sequencestructural observation is necessary in conservative positions analysis, active and binding site residues, variation studies, alignments, classification and identification of the key residues for protein functionality, formation of macromolecular complexes and in evolutionary distance analysis. Thus, complete applications that incorporate data from different sources create possible in visualization and help in analytical studies are an everyday requirement in biology, biochemistry, molecular biology and related research areas (Abyzov et al., 2005).

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J. Atoms and Molecules/ 3(5); 2013 / 576578 Appropriate visualization of scientific data is essential in structural biology, where researchers search for to achieve an understanding of the overall structure and function of biological macromolecules of interest. In the last decade numerous visualization programs are developed which enable observation of biological macromolecules. It is important to have access the visualization programs which are fast, flexible, and customizable. Excellent visualizations offer researchers sensitive feel to understand the behavior of molecules. On the other hand, simultaneously it is also important for such programs to be capable to show 3D annotations of errors in the models or interaction sites (Chen et al., 2009). Generally structural bioinformaticians make use of composite graphics software to put on view a variety of representations of the macromolecular structures. Coordinates are deposited in the Protein Data Bank (PDB), if the structure determination is complete. Molecular graphics plays an important role in the determination of protein structures using X-ray crystallographic data and NMR, even with continuing efforts to automate model building such as side-chain placement, loop, ligand and fragment fitting, structure comparison, analysis and validation are routinely performed using molecular graphics. As possible researchers intend to build their analyses as objective and quantitative whereas visualization software is primarily used to make subjective assessments that guide computational modeling. While existing algorithmic methods are not sufficient for viewing software is also used for interactive investigation. Images and animations are used to present last outcome. A practical assess of usefulness for visualization software is its extensive usefulness in achieving significant biological results. Research developers are All rights reserved 2011

Barik BP mainly disturbed with biology or methodology somewhat than widespread use of their software, new visualization methods have value only in mixture with old ones and required data standards are missing (Goddard and Ferrin, 2007). Many visualization tools are present and representations are consistent for protein structures whereas by the use of tools viewing of macromolecular structures is improved so as to best fraction of molecular features. It is a tackle of visualization methods to display and highlight key concepts and features and maintaining the exactness of the data (Couch et al., 2006). The aim of modern bioinformatics studies is to divulge biological and biochemical functions of individual biomolecules based on their threedimensional structures. In view of that, researchers have focused on the protein molecular surfaces, where for the most part functional activity occurs also for molecular recognition, electrostatic properties are measured important (Kinoshita, 2004). There is a wide variety of molecular visualization tools available, which makes an exhaustive search of all of them impossible. The common programs which works both in windows and linux operating systems are Rasmol, RasTop, Jmol, Swisspdb viewer, CN3D, Chimera, DeepView, Doscovery studio, MarvinSpace, Molegro, MOLMOL, AstexViewer, NOC, PyMOL, QuteMol, VMD and Yasara etc to name a few. REFERENCES: 1) Abyzov A., Errami M, Leslin C.M. and Ilyin V.A. (2005). Friend, an integrated analytical front-end application for Bioinformatics. Bioinformatics, 21(18): 36773678. 2) Chen V.B., Davis I.W. and Richardson D.C. (2009). KING (Kinemage, Next Generation): A versatile interactive www.jamonline.in 577

J. Atoms and Molecules/ 3(5); 2013 / 576578 molecular and scientific visualization program, Protein Science, 18(11): 2403 2409. 3) Couch G.S., Hendrix D.K. and Ferrin T.E. (2006). Nucleic acid visualization with UCSF Chimera, Nucleic Acids Research, 34(4): e29.

Barik BP 4) Goddard T.D. and Ferrin T.E. (2007). Visualization software for molecular assemblies. Current Opinion in Structural Biology, 17 (5): 587595. 5) Kinoshita K, and Nakamura H. (2004). eF-site and PDBjViewer: database and viewer for protein functional sites, Bioinformatics, 20(8): 13291330.

How to cite this article: Bibhuti P. Barik Computational visualization of biomolecular structures J. Atoms and Molecules, 3(5), 2013: 576 578. All rights reserved 2011 www.jamonline.in 578