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Bioinformatics Advance Access originally published online on February 25, 2007
Bioinformatics 2007 23(8):1035-1037; doi:10.1093/bioinformatics/btm067
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SwS: a solvation web service for nucleic acids

Pascal Auffinger * and Yaser Hashem

A.R.N., Université Louis Pasteur, IBMC-CNRS, 15 rue René Descartes, 67084 Strasbourg, France

*To whom correspondence should be addressed.


  Abstract

Summary: SwS, based on a statistical analysis of crystallographic structures deposited in the NDB, is designed to provide an exhaustive overview of the solvation of nucleic acid structural elements through the generation of 3D solvent density maps. A first version (v1.0) of this web service focuses on the interaction of DNA, RNA and hybrid base pairs linked by two or three hydrogen bonds with water, cations and/or anions. Data provided by SwS are updated on a weekly basis and can be used by: (i) those involved in molecular dynamics simulation studies for validation purposes; (ii) crystallographers for help in the interpretation of solvent density maps; and all those involved in (iii) drug design and, more generally, in (iv) nucleic acid structural studies. SwS provides also statistical data related to the frequency of occurrence of different types of base pairs in crystallographic structures and the conformation of the involved nucleotides. This web service has been designed to allow a maximum of flexibility in terms of queries and has also been developed with didactic considerations in mind.

Availability: http://www-ibmc.u-strasbg.fr/arn/sws.html

Contact: p.auffinger{at}ibmc.u-strasbg.fr

Associate Editor: Keith Crandall

Received on January 30, 2007; accepted on February 20, 2007

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