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Welcome to SLITHER
A web server for generating contiguous conformations of
substrate molecules entering into
deep active sites of proteins
or migrating across membrane transporters
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. Specific substrates of membrane transporters can
migrate to another side of cellular compartment. SLITHER 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 the
HOLE program
that is 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.
Reference: Po-Hsien Lee, Kuei-Ling Kuo, Pei-Ying Chu, Eric M. Liu, Jung-Hsin Lin*. 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. Nucleic Acids Research 37: W559-W564 (2009)
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