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ModLoop: automated modeling of loops in protein structures
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Abstract
ModLoop is a web server for automated modeling of loops in protein structures. The
input is the atomic coordinates of the protein structure in the Protein Data Bank
format, and the specification of the starting and ending residues of one or more segments
to be modeled, containing no more than 20 residues in total. The output is the coordinates
of the non-hydrogen atoms in the modeled segments. A user provides the input to the
server via a simple web interface, and receives the output by e-mail. The server relies
on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction
of spatial restraints, without relying on a database of known protein structures.
For a rapid response, ModLoop runs on a cluster of Linux PC computers.
The server is freely accessible to academic users at http://salilab.org/modloop