Development of Neighbors Atomic Coordinate Tables and Plot-Graphical Representation for Tertiary Structure in Proteins
Nawal T.Alomousha, Jehad Q. Odeha, Hamed J. Al-Fawarehb
aDepartment of Computer Science
Prince Hussein Bin Abdullah Information Technology Collage
Al al-Bayt University
Jordan
bDepartment of Software Engineering
Faculty of Science and IT
Zarqa Private University, Zarqa
Jordan
Abstract
This paper developed a method to predict a protein 3D structure from the amino acid sequence using contact map, the method shows prediction a protein in a binary space of exposure states. The 3D structure of protein can be represented using symmetrical binary matrix C called contact map whose element C (i, j) =1 when the physical distance between amino acid i and j is less than or equal to a pre assigned threshold t. Contact map used for solvent accessibility predictions. In view of this a direct random coordinate was desired, in terms of the contribution of atomic neighbors in making them exposed to predict a protein 3D structure. Present work aims to prediction of a protein 3D structure from contact map, how the random prediction of an atomic coordinate is affected by the change threshold t in a neighboring residue, or other positions of these residues. In addition, a graphical method of representing a protein 3D structure was developed.