On the reconstruction of three-dimensional protein structures from contact maps

DOI10.3390/A2010076MaRDI QIDQ1662462zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Pietro Di Lena, Marco Vassura, Luciano Margara, Piero Fariselli, R. Casadio

Publication date 20 August 2018

Published in Algorithms (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.3390/a2010076

zbMATH Keywords

contact mapmolecular modelingprotein folding

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Review text

Summary: 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.

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Cited in

(3)

• Ab-initio computation of the 3d-structures of proteins by nonparametric statistical methods -- medium and short range distance estimates
• Advances in Neural Networks – ISNN 2005
• Evolutionary decision rules for predicting protein contact maps

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• FT-COMAR

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