Evaluating the usefulness of protein structure models for molecular replacement

MOTIVATION We investigate the relationship between the quality of models of protein structure and their usefulness as search models in molecular replacement, a widely used method to experimentally determine protein structures by X-ray crystallography. RESULTS We used the available models submitted to the Critical Assessment of Techniques for Protein Structure Prediction to verify in which cases they can be automatically used as search templates for molecular replacement. Our results show that there is a correlation between the quality of the models and their suitability for molecular replacement but that the traditional method of relying on sequence identity between the model and the template used to build it is not diagnostic for the success of the procedure. AVAILABILITY Additional data are available at http://cassandra.bio.uniroma1.it/mr-results-casp.html

[1]  B. Rost,et al.  Critical assessment of methods of protein structure prediction (CASP)—Round 6 , 2005, Proteins.

[2]  T. Hubbard,et al.  Critical assessment of methods of protein structure prediction (CASP): Round III , 1999, Proteins.

[3]  Richard J Morris,et al.  ARP/wARP's model-building algorithms. I. The main chain. , 2002, Acta crystallographica. Section D, Biological crystallography.

[4]  S. Bryant,et al.  Critical assessment of methods of protein structure prediction (CASP): Round II , 1997, Proteins.

[5]  Peter Briggs,et al.  A graphical user interface to the CCP4 program suite. , 2003, Acta crystallographica. Section D, Biological crystallography.

[6]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[7]  D. Blow,et al.  The detection of sub‐units within the crystallographic asymmetric unit , 1962 .

[8]  Alfonso Valencia,et al.  Protein Refinement: A New Challenge For Casp In Its 10th Anniversary , 2005, Bioinform..

[9]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[10]  C. Sander,et al.  Errors in protein structures , 1996, Nature.

[11]  M Wilmanns,et al.  Molecular replacement with NMR models using distance-derived pseudo B factors. , 1996, Acta crystallographica. Section D, Biological crystallography.

[12]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[13]  Anna Tramontano,et al.  Ten years of predictions … and counting , 2005, The FEBS journal.

[14]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[15]  T. Hubbard,et al.  Critical assessment of methods of protein structure prediction (CASP)‐round V , 2003, Proteins.

[16]  K Fidelis,et al.  A large‐scale experiment to assess protein structure prediction methods , 1995, Proteins.

[17]  D. T. Jones,et al.  Evaluating the potential of using fold-recognition models for molecular replacement. , 2001, Acta crystallographica. Section D, Biological crystallography.

[18]  L. Lally.  The CCP 4 Suite — Computer programs for protein crystallography , 1998 .

[19]  D. Eisenberg,et al.  VERIFY3D: assessment of protein models with three-dimensional profiles. , 1997, Methods in enzymology.

[20]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .

[21]  Jean-Michel Claverie,et al.  CaspR: a web server for automated molecular replacement using homology modelling , 2004, Nucleic Acids Res..

[22]  E J Dodson,et al.  Modern developments in molecular replacement. , 1996, Current opinion in structural biology.