Next Article in Journal
A Survey on Star Identification Algorithms
Next Article in Special Issue
Algorithm for Nanotubes Computer Generation with Different Configurations
Previous Article in Journal
A Novel Block-based Watermarking Scheme Using the SVD Transform
Previous Article in Special Issue
Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels
Article Menu

Export Article

Open AccessReview

On the Reconstruction of Three-dimensional Protein Structures from Contact Maps

Department of Computer Science, University of Bologna, Via Mura Anteo Zamboni, 7, 40127 Bologna, Italy
Biocomputing Group, Department of Biology, University of Bologna, Via Irnerio, 42, 40127 Bologna, Italy
Author to whom correspondence should be addressed.
Algorithms 2009, 2(1), 76-92;
Received: 30 November 2008 / Revised: 8 January 2009 / Accepted: 20 January 2009 / Published: 22 January 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
PDF [240 KB, uploaded 22 January 2009]


The problem of protein structure prediction is one of the long-standing goals of Computational Biology. Although we are still not able to provide first principle solutions, several shortcuts have been discovered to compute the protein three-dimensional structure when similar protein sequences are available (by means of comparative modeling and remote homology detection). Nonetheless, these approaches can assign structures only to a fraction of proteins in genomes and ab-initio methods are still needed. One relevant step of ab-initio prediction methods is the reconstruction of the protein structures starting from inter-protein residue contacts. In this paper we review the methods developed so far to accomplish the reconstruction task in order to highlight their differences and similarities. The different approaches are fully described and their reported performances, together with their computational complexity, are also discussed. View Full-Text
Keywords: Protein folding; contact map; molecular modeling Protein folding; contact map; molecular modeling
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

Share & Cite This Article

MDPI and ACS Style

Di Lena, P.; Vassura, M.; Margara, L.; Fariselli, P.; Casadio, R. On the Reconstruction of Three-dimensional Protein Structures from Contact Maps. Algorithms 2009, 2, 76-92.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Algorithms EISSN 1999-4893 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top