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Open Access Research article

Optimal contact definition for reconstruction of Contact Maps

Jose M Duarte12*, Rajagopal Sathyapriya1, Henning Stehr1, Ioannis Filippis13 and Michael Lappe1

Author Affiliations

1 Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany

2 Laboratory of Biomolecular Research, Paul Scherer Institut, 5232 Villigen PSI, Switzerland

3 Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK

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BMC Bioinformatics 2010, 11:283  doi:10.1186/1471-2105-11-283

Published: 27 May 2010



Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure.


We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the Cβ atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity.


Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap.