Reconstruction of 3D Structures From Protein Contact Maps

• 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
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2008.27

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.