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Copyright © 2012 | AIZEON publishers | All rights reserved

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Journal of Bioinformatics and Research 1(4) 2012: 41-45

Tips for loop prediction and conformational search


Jamal Raiyn, Mohammed Azab, Mahmud Masalha and Anwar Rayan1*

1Drug Discovery Informatics Lab, QRC-Qasemi Research Center,Al-Qasemi Academic College, P.O.B. 124, Baka El-Garbiah 30100,
Israel.

* To whom correspondence should be addressed. Email: a_rayan@qsm.ac.il

ABSTRACT

The 3D structure determination of a protein is crucial for structure-guided drug development and the homology modeling approach is the most accurate method among the computational methods, yielding reliable models. Loop predictions are required in many protein homology modeling studies and raise the problem of loop closure. Loop closure problems have been solved mainly by “ab-initio” methods or by employing databases. “ab-initio” methods mostly use standard bond lengths and angles. However, backbone bonds and angles are not standard in different crystallographic structures, thus, is it possible to achieve high quality loop closure by employing standard bond lengths and angles? To explore this issue we reconstructed loops from the structurally refined proteins with standard parameters but retained the experimental backbone dihedral angles. This was tested by stepwise construction from one of the terminals (N- and C-) toward the other as well as from both terminals towards the center. We conclude that introducing variability for bond lengths, for bond angles and for omega dihedrals, is essential for accurate prediction of loops. As well, constructing loops from both terminals toward the center give
more precise models, closer to native structures.


Copyright © 2012 | AIZEON publishers | All rights reserved

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Citation: Raiyn J, Azab M, Masalha M and Rayan A (2012). Tips for loop prediction and conformational search. Journal of Bioinformatics and Research 1(4): 41-45

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