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Paper   IPM / Biological / 13211
School of Biological Sciences
  Title:   The Interpretation Of Protein Structures Based On Graph Theory And Contact Map
1.  M. Habibi.
2.  C. Eslahchi.
3.  M. Sadeghi.
4.  H. Pezeshk.
  Status:   Published
  Journal: Open Access Bioinformatics
  Vol.:  2
  Year:  2010
  Pages:   127-137
  Supported by:  IPM
Purpose: The analysis of a protein’s structure allowing detailed exploration of the protein’s biological function is one of the most challenging problems in bioinformatics. There are efficient algorithms to calculate main properties of a protein structure, such as packing density, buried or surface residues, and accessible surface area. But these algorithms need the three-dimensional (3D) coordinates of the proteins. Methods: We used the contact map of a protein to construct a graph. By considering several features of the corresponding graph, we proposed some algorithms to discuss the above- mentioned properties of a protein. We also introduced a new measure for the hydrophobicity of an amino acid by defining an average degree for the amino acid as a vertex on the graph. Results: We compared our results with those obtained by some other existing algorithms. We found strong correlations between the popular methods, which use 3D coordinates, and our methods, which only use a predicted contact map. Conclusion: Many features of a protein can be predicted without having 3D coordinates, based on the contact map of the protein. The programs are freely available from http://www.bioinf. cs.ipm.ir/softwares/asa/asa.rar.

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