Exact methods for lattice protein models

Mann, M.; Backofen, R.

doi:10.1515/bams-2014-0014

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Tytuł artykułu

Exact methods for lattice protein models

Autorzy

Mann M. , Backofen R.

Wybrane pełne teksty z tego czasopisma

Identyfikatory

DOI

10.1515/bams-2014-0014

Warianty tytułu

Języki publikacji

Abstrakty

Lattice protein models are well-studied abstractions of globular proteins. By discretizing the structure space and simplifying the energy model over regular proteins, they enable detailed studies of protein structure formation and evolution. However, even in the simplest lattice protein models, the prediction of optimal structures is computationally difficult. Therefore, often, heuristic approaches are applied to find such conformations. Commonly, heuristic methods find only locally optimal solutions. Nevertheless, there exist methods that guarantee to predict globally optimal structures. Currently, only one such exact approach is publicly available, namely the constraint-based protein structure prediction method and variants. Here, we review exact approaches and derived methods. We discuss fundamental concepts like hydrophobic core construction and their use in optimal structure prediction, as well as possible applications like combinations of different energy models.

Słowa kluczowe

CPSP HP-model lattice protein optimal structure protein structure prediction

Wydawca

Uniwersytet Jagielloński - Collegium Medicum
Index Copernicus Sp. z o.o.

Czasopismo

Bio-Algorithms and Med-Systems

Rocznik

2014

Tom

Vol. 10, no. 4

Strony

213--225

Opis fizyczny

Bibliogr. 95 poz., rys., wykr.

Twórcy

autor

Mann M.

mmann@informatik.uni-freiburg.de

Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany

autor

Backofen R.

backofen@informatik.uni-freiburg.de

Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark

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