A constraint-based approach to fast and exact structure prediction in three-dimensional protein models

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A constraint-based approach to fast and exact structure prediction in three-dimensional protein models (2006)

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by Rolf Backofen , Sebastian Will

Venue:	J. of Constraints
Citations:	46 - 12 self

BibTeX

@ARTICLE{Backofen06aconstraint-based,
    author = {Rolf Backofen and Sebastian Will},
    title = {A constraint-based approach to fast and exact structure prediction in three-dimensional protein models},
    journal = {J. of Constraints},
    year = {2006},
    volume = {11},
    pages = {2006}
}

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Abstract

Simplified protein models are used for investigating general properties of proteins and principles of protein folding. Furthermore, they are suited for hierarchical approaches to protein structure prediction. A well known protein model is the HPmodel of Lau and Dill [33], which models the important aspect of hydrophobicity. One can define the HP-model for various lattices, among them two-dimensional and three-dimensional ones. Here, we investigate the three-dimensional case. The main motivation for studying simplified protein models is to be able to predict model structures much more quickly and more accurately than is possible for real proteins. However, up to now there was a dilemma: the algorithmically tractable, simple protein models can not model real protein structures with good quality and introduce strong artifacts. We present a constraint-based method that largely improves this situation. It outperforms all existing approaches for lattice protein folding in HP-models. This approach is the first one that can be applied to two three-dimensional lattices, namely the cubic lattice and the face-centered-cubic (FCC) lattice. Moreover, it is the only exact method for the FCC lattice. The ability to use the FCC lattice is a significant improvement over the cubic lattice. The key to our approach is the ability to compute maximally compact sets of points (used as hydrophobic cores), which we accomplish for the first time for the FCC lattice. Keywords: protein structure prediction, HP-model, face-centered cubic lattice, constraint programming 1.

Keyphrases

structure prediction constraint-based approach three-dimensional protein model fcc lattice protein model cubic lattice real protein model structure strong artifact three-dimensional one exact method general property significant improvement various lattice protein folding hydrophobic core face-centered cubic lattice hierarchical approach three-dimensional case first one three-dimensional lattice important aspect protein structure prediction good quality main motivation simple protein model first time simplified protein model lattice protein compact set constraint-based method

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