Unit disk graph recognition is NP-hard
Computational Geometry: Theory and Applications - Special issue on geometric representations of graphs
Introduction to Algorithms
Distance Geometry Optimization for Protein Structures
Journal of Global Optimization
Introduction to Bioinformatics
Introduction to Bioinformatics
Reconstruction of 3D structures from protein contact maps
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Unconventional training for neural network predictions of inter-residue contacts
Proceedings of the 1st ACM workshop on Breaking frontiers of computational biology
Computational Intelligence Methods for Bioinformatics and Biostatistics
Methods to predict protein spatial structure
Cybernetics and Systems Analysis
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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 Ångstroms allow reconstructing 3D models that are very similar to the proteins native structure.