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CaspR: a web server for automated molecular replacement using homology modelling.

Jean-Baptiste Claude1, Karsten Suhre, Cédric Notredame

  • 1Information Génomique & Structurale (UPR CNRS 2589), Institut de Biologie Structurale et Microbiologie, 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.

Nucleic Acids Research
|June 25, 2004
PubMed
Summary

CaspR automates molecular replacement (MR) by screening numerous homology models, increasing the success rate for X-ray crystallography structure determination, especially for low-sequence similarity targets.

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Area of Science:

  • Structural biology
  • X-ray crystallography
  • Computational biology

Background:

  • Molecular replacement (MR) is a key technique for X-ray crystallography structure determination.
  • MR success rates decline significantly with less than 35% sequence identity between template and target proteins.

Purpose of the Study:

  • To present CaspR, a web tool automating MR by screening multiple homology models.
  • To enhance the success rate of MR, particularly for targets with low sequence similarity to known structures.

Main Methods:

  • CaspR integrates T-COFFEE for alignments, MODELLER for homology modeling, AMoRe for MR, and CNS for refinement.
  • The automated protocol generates multiple structure-sequence alignments and homology models.
  • It performs MR and provides pre-refined structures for download.

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Main Results:

  • CaspR significantly increases the fraction of protein structures solvable by MR.
  • Automated screening of homology models improves MR success for low-similarity targets.
  • Pre-refined models from CaspR reduce the time needed for structure refinement.

Conclusions:

  • CaspR offers an automated and effective strategy to overcome limitations in traditional MR.
  • This approach is expected to boost the throughput of structural genomics projects.
  • The web tool provides a valuable resource for protein structure determination.