Briefings in Bioinformatics Advance Access published online on March 30, 2009
Briefings in Bioinformatics, doi:10.1093/bib/bbp013
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2D molecular graphics: a flattened world of chemistry and biology
Corresponding author. Zhicai Shang, Department of Chemistry, Zhejiang University, Hangzhou 310027, China. Tel: +86 571 87952379; Fax: +86 571 87951895; E-mail: shangzc{at}zju.edu.cn.
Molecular graphics provides an intuitive way for representation, modeling and analysis of complex chemical and biological systems. It is now widely used in the theoretical chemistry, structural biology, molecular modeling and drug design communities. Traditional molecular graphics techniques mainly dedicate to showing molecular architectures at three-dimensional (3D) level. However, in some occasions the two-dimensional (2D) representation of molecular configurations, profiles, behaviors and interactions may be more readily acceptable for audiences, especially when we need to describe abstract information in a straightforward way or to present numerous data in schematic diagrams. In recent years, 2D representation methods/tools have been developed rapidly for various purposes, ranging from the aesthetic depiction of atomic arrangement for small organic molecules to schematic layout of complicated nonbonding network across the biomolecular binding interfaces, and have received considerable interest in the fields of chemistry, biology and medicine. In this article we first propose the term of 2D molecular graphics to cover the spectrum of 2D representing chemical and biological systems, we also give a comprehensive review on the methods, tools and applications of 2D molecular graphics.
Keywords: 2D molecular graphics, schematic diagram, chemical and biological system, bioinformatics
Submitted: December 31, 2008. Received (in revised form): February 17, 2009.