molvie: an interactive visualization environment for molecular structures

A Molecular visualization interactive environment ( molvie), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of molvie, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in java, molvie is platform-independent. Moreover, it may run on a webpage as an applet for remote users. molvie is available at http://www.cs.ucsb.edu/∼mli/Bioinf/software/index.html.