MolAxis: a server for identification of channels in macromolecules.

Eitan Yaffe*, Dan Fishelovitch, Haim J. Wolfson, Dan Halperin, Ruth Nussinov

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

53 Scopus citations


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

Original languageEnglish
Pages (from-to)W210-215
JournalNucleic Acids Research
Issue numberWeb Server issue
StatePublished - 1 Jul 2008


FundersFunder number
National Institutes of HealthN01-CO-12400
National Cancer InstituteZIABC010442
Israel Science Foundation236/ 06
Tel Aviv University


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