Abstract

Summary: 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.

Availability: The server is freely accessible to academic users at http://salilab.org/modloop

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Author notes

1Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA and 2Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California, San Francisco, CA 94143-2240, USA

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