ModLoop: Automated modeling of loops in protein structures

András Fiser, Andrej Sali

Research output: Contribution to journalArticle

433 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)2500-2501
Number of pages2
JournalBioinformatics
Volume19
Issue number18
DOIs
StatePublished - Dec 12 2003

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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