WAP: water analysis package - a Web-based package to calculate geometrical parameters between water oxygen and protein atoms

Shanthi, V and Rajesh, CK and Jayalakshmi, J and Vijay, VG and Sekar, K (2003) WAP: water analysis package - a Web-based package to calculate geometrical parameters between water oxygen and protein atoms. In: Journal of Applied Crystallography, 36 (1). pp. 167-168.

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Abstract

With the advent of Internet computing and World Wide Web technology, Web browsers have provided powerful tools for server and client-side applications. Exploiting this rapidly growing technology, the Water Analysis Package (WAP) has been developed to enable the user to calculate geometrical parameters between water oxygen atoms and a user-specified region in a given protein or nucleic acid structure. In fact, there are few stand-alone programs (for example the CONTACT module available in the CCP4 suite of programs; Collaborative Computational Project, Number 4, 1994) to calculate geometrical parameters involving water molecules and protein atoms. Furthermore, the available programs do not provide the user with flexible options to perform a specific task. These programs in general require the Protein Data Bank (PDB) (Bernstein et al., 1977) file containing the atomic coordinates, the unit-cell constants and the space-group information. To the best of our knowledge, there is no program available on the Web to perform the above task for structures deposited in the PDB or available in the public domain. At present, the PDB is maintained by the Research Collaboratory in Structural Bioinformatics (RCSB) at the Rutgers University, New Jersey, USA (Berman et al., 2000).

Item Type:	Journal Article
Publication:	Journal of Applied Crystallography
Publisher:	International Union of Crystallography
Additional Information:	Copyright of this article belongs to International Union of Crystallography.
Keywords:	protein crystallography;macromolecular crystallography; Protein Data Bank;computer programs
Department/Centre:	Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited:	02 Jun 2006
Last Modified:	19 Sep 2010 04:28
URI:	http://eprints.iisc.ac.in/id/eprint/7319

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