ModLoop: automated modeling of loops in protein structures | Zendy

András Fiser | Zendy; Andrej Šali | Zendy

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ModLoop: automated modeling of loops in protein structures

Author(s) -

András Fiser,

Andrej Šali

Publication year - 2003

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btg362

Subject(s) - modeller , computer science , loop (graph theory) , interface (matter) , simple (philosophy) , web server , software , protein data bank , user interface , operating system , protein structure , database , algorithm , the internet , chemistry , mathematics , biochemistry , philosophy , bubble , epistemology , combinatorics , maximum bubble pressure method , homology modeling , enzyme

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.

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