Reconstruction of 3D Structures From Protein Contact Maps

The prediction of the protein tertiary structure from solely its residue sequence (the so called Protein Folding Problem) is one of the most challenging problems in Structural Bioinformatics. We focus on the protein residue contact map. When this map is assigned it is possible to reconstruct the 3D...

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Bibliographic Details
Published in:IEEE/ACM transactions on computational biology and bioinformatics 2008-07, Vol.5 (3), p.357-367
Main Authors: Vassura, M., Margara, L., Di Lena, P., Medri, F., Fariselli, P., Casadio, R.
Format: Article
Language:English
Subjects:
Binding Sites
Bioinformatics
Combinatorial algorithms
Computer Simulation
Contact map
Cost function
Heuristic algorithms
Models, Chemical
Models, Molecular
Molecular Modeling
Nuclear magnetic resonance
Predictive models
Protein Binding
Protein Conformation
Protein Folding
Protein Interaction Mapping - methods
Protein structure prediction
Proteins
Proteins - chemistry
Proteins - ultrastructure
Simulated annealing
Solvents
Spine
US Department of Transportation
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Summary:The prediction of the protein tertiary structure from solely its residue sequence (the so called Protein Folding Problem) is one of the most challenging problems in Structural Bioinformatics. We focus on the protein residue contact map. When this map is assigned it is possible to reconstruct the 3D structure of the protein backbone. The general problem of recovering a set of 3D coordinates consistent with some given contact map is known as a unit-disk-graph realization problem and it has been recently proven to be NP-Hard. In this paper we describe a heuristic method (COMAR) that is able to reconstruct with an unprecedented rate (3-15 seconds) a 3D model that exactly matches the target contact map of a protein. Working with a non-redundant set of 1760 proteins, we find that the scoring efficiency of finding a 3D model very close to the protein native structure depends on the threshold value adopted to compute the protein residue contact map. Contact maps whose threshold values range from 10 to 18 Aringngstroms allow reconstructing 3D models that are very similar to the proteins native structure.
ISSN:1545-5963
1557-9964
DOI:10.1109/TCBB.2008.27