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A resource for benchmarking the usefulness of protein structure models

Daniel Carbajo1 and Anna Tramontano123*

Author Affiliations

1 Department of Physics, Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy

2 Institut Pasteur Fondazione Cenci-Bolognetti, Rome, Italy

3 Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy

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BMC Bioinformatics 2012, 13:188  doi:10.1186/1471-2105-13-188

Published: 2 August 2012



Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application.


This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively.


The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database.

Implementation, availability and requirements

Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: webcite

Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

Protein structure prediction; Decoy database; Comparative modeling; ModelDB