“School of Biological Sciences”
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| Paper IPM / Biological Sciences / 13211 |
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Purpose: The analysis of a proteinâs structure allowing detailed exploration of the proteinâs
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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