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Nucleic Acids Research Advance Access published online on April 29, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn223
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© 2008 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.

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MolAxis: a server for identification of channels in macromolecules

Eitan Yaffe1, Dan Fishelovitch2, Haim J. Wolfson1, Dan Halperin1,* and Ruth Nussinov2,3

1School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, 2Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel and 3SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI – Frederick, Bldg 469, Rm 151, Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +972-3-6406478; Fax: +972-3-6405387; Email: danha{at}post.tau.ac.il Correspondence may also be addressed to Ruth Nussinov. Tel: 301-846-5579; Fax: 301-846-5598; Email: ruthn{at}ncifcrf.gov

Received February 11, 2008. Revised April 3, 2008. Accepted April 10, 2008.

MolAxis is a freely available, easy-to-use web server for identification of channels that connect buried cavities to the outside of macromolecules and for transmembrane (TM) channels in proteins. Biological channels are essential for physiological processes such as electrolyte and metabolite transport across membranes and enzyme catalysis, and can play a role in substrate specificity. Motivated by the importance of channel identification in macromolecules, we developed the MolAxis server. MolAxis implements state-of-the-art, accurate computational-geometry techniques that reduce the dimensions of the channel finding problem, rendering the algorithm extremely efficient. Given a protein or nucleic acid structure in the PDB format, the server outputs all possible channels that connect buried cavities to the outside of the protein or points to the main channel in TM proteins. For each channel, the gating residues and the narrowest radius termed ‘bottleneck’ are also given along with a full list of the lining residues and the channel surface in a 3D graphical representation. The users can manipulate advanced parameters and direct the channel search according to their needs. MolAxis is available as a web server or as a stand-alone program at http://bioinfo3d.cs.tau.ac.il/MolAxis.


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