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Nucleic Acids Research Advance Access originally published online on May 11, 2009
Nucleic Acids Research 2009 37(Web Server issue):W559-W564; doi:10.1093/nar/gkp359
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W559-W564
© 2009 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.

Articles

SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters

Po-Hsien Lee1, Kuei-Ling Kuo2, Pei-Ying Chu1, Eric M. Liu2 and Jung-Hsin Lin1,2,3,*

1Division of Mechanics, Research Center for Applied Sciences, Academia Sinica,2School of Pharmacy, National Taiwan University and 3Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan

*To whom correspondence should be addressed. Tel: +886 2 2782 3212, ext. 886; Fax: +886 2 2782 3060; Email: jlin{at}ntu.edu.tw;jhlin{at}gate.sinica.edu.tw

Received March 8, 2009. Revised April 19, 2009. Accepted April 23, 2009.

Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design.


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