ModLoop: Automated modeling of loops in protein structures

Andras Fiser, Andrej Sali

Research output: Contribution to journalArticle

425 Citations (Scopus)

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

Fingerprint

Protein Structure
Proteins
Servers
Server
Modeling
Protein Databases
Output
Web Server
Postal Service
Linux
Electronic Mail
Conformation
Databases
Specification
Interfaces (computer)
Protein
Conformations
Predict
Specifications
Atoms

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

ModLoop : Automated modeling of loops in protein structures. / Fiser, Andras; Sali, Andrej.

In: Bioinformatics, Vol. 19, No. 18, 12.12.2003, p. 2500-2501.

Research output: Contribution to journalArticle

Fiser, Andras ; Sali, Andrej. / ModLoop : Automated modeling of loops in protein structures. In: Bioinformatics. 2003 ; Vol. 19, No. 18. pp. 2500-2501.
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