WAP (version 2.0): an updated computing and visualization server for water molecules

摘要

By exploiting the fast-growing Internet technology, the interactive computing server Water Analysis Package (WAP, version 2.0) has been updated with more flexible options to better understand the role of the water O atoms present in three-dimensional macromolecular (protein or nucleic acid) structures. The updated robust server facilitates the computation and visualization of water molecules from various hydration shells, interfacial water molecules and those water molecules that stabilize various secondary structural elements. It is also possible to detect the interactions of water molecules with various parts (polar atoms, nonpolar atoms, main-chain and side-chain atoms) of the protein molecule. Furthermore, a molecular graphics visualization program is interfaced to display the nature of the interactions of the water molecules. The Protein Data Bank archive interfaced with the server is updated every week; hence users get to analyse the latest structures. The computing server can be obtained from http://dicsoft2.physics.iisc.ernet.in/wap/. (c) 2008 International Union of Crystallography Printed in Singapore - all rights reserved.