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Related Experiment Video

Updated: Jul 18, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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Automatic procedure for using models of proteins in molecular replacement.

Domenico Raimondo1, Alejandro Giorgetti, Alejandro Giorgetti

  • 1Department of Biochemical Sciences, University of Rome La Sapienza, P.le Aldo Moro, 5-00185 Rome, Italy.

Proteins
|November 17, 2006
PubMed
Summary

Predicting protein structures for molecular replacement is challenging. This new method quickly assesses if computational models can solve structures, achieving success in over half of tested cases.

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Last Updated: Jul 18, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Structural biology
  • X-ray crystallography
  • Computational biology

Background:

  • Molecular replacement is crucial for determining protein structures from X-ray diffraction data.
  • Accurate atomic models are required for successful molecular replacement.
  • Predicting the quality of computational models for molecular replacement is difficult.

Purpose of the Study:

  • To develop a rapid method for assessing the suitability of protein structures for molecular replacement using computational models.
  • To improve the success rate of structure determination via molecular replacement.

Main Methods:

  • Submitting target protein sequences to multiple structure prediction servers.
  • Clustering resulting models and selecting representative structures.
  • Utilizing these representative structures as search models in an automated phasing pipeline.
  • Testing the procedure with newly released protein structure factors from the Protein Data Bank.

Main Results:

  • The automated procedure successfully generated interpretable electron density maps in over 50% of cases.
  • This method provides a quick assessment of molecular replacement feasibility.
  • The approach leverages freely available computational tools.

Conclusions:

  • The developed method offers a practical solution for evaluating the potential of computational models in molecular replacement.
  • This can streamline the structure determination process in X-ray crystallography.
  • Further refinement of computational modeling and assessment tools is warranted.