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

Algorithms

Pietro Di Lena¹  Marco Vassura¹  Luciano Margara¹  Piero Fariselli² 

[1] 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 E-mails: {dilena, vassura, margara}@cs.unibo.it; [e-mail]; [e-mail]

关键词: Protein folding;    contact map;    molecular modeling;   

DOI  :  10.3390/a2010076

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.