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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.
Received: 30 November 2008; in revised form: 8 January 2009 / Accepted: 20 January 2009 / Published: 22 January 2009
Abstract: 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.
Keywords: Protein folding; contact map; molecular modeling
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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.
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(1):76-92.
Di Lena, Pietro; Vassura, Marco; Margara, Luciano; Fariselli, Piero; Casadio, Rita. 2009. "On the Reconstruction of Three-dimensional Protein Structures from Contact Maps." Algorithms 2, no. 1: 76-92.