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Copyright © 2012 | AIZEON publishers | All rights reserved

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ABSTRACT   REFERENCES  
Journal of Bioinformatics and Research 1(1) 2012: 10-14

Computational analysis of active site amino acid dihedral angles of CDK2 towards ligand binding


Srinivasu Nulaka1* and Appa Rao Allam2

1Department of Computer Science (MCA), KGRL College, Bhimavaram, AP, India. E-mail: nulaka@gmail.com
2Vice-chancellor, JNTUK, Kakinada, AP, India E-mail : apparaoallam@gmail.com

* To whom correspondence should be addressed. Email: nulaka@gmail.com

ABSTRACT

Cell proliferation is a consequence of positive signals which promote cell division and negative signals which suppress the process. Key factors in this signaling cascade are a series of cyclin dependent kinases (CDKs). It has been identified experimentally that CDK enzymes are highly flexible and the ligand binding orientations are primarily influenced by side chain torsions of amino acids in active site region. Hence to address the importance of backbone and side chain phi, psi and chi angle contributions upon ligand binding, various computational softwares and approaches have been utilized to recognize the influential dihedral angles towards ligand binding. The dihedrals angles (phi, psi, chi1, chi2, chi3, chi4) of all 135 enzymes from protein data bank were calculated using DANG software. The effect of changes in the backbone and side chain torsion angles (phi, psi and chi) on ligand binding within CDK2 is predicted using multiple regression analysis. After removing few data as outliers, 121 proteins as training set and 7 proteins as validation (test) set resulted in 19 variable model with regression coefficient, r: 0.765 R^2: 0.586 and Cross Validation, r^2(CV): 0.977. The results showed that 19 out of 85 independent variables (torsion angles) are highly influential towards ligand binding with in CDK2 proteins.

Copyright © 2012 | AIZEON publishers | All rights reserved

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Citation: Nulaka S and Allam AR (2012). Computational analysis of active site amino acid dihedral angles of CDK2 towards ligand binding. Journal of Bioinformatics and Research 1(1): 10-14

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