HOW MUCH SEQUENCE IDENTITY GUARANTEE GOOD MODELS IN HOMOLOGY MODELING - Proteins from Serine Protease Family as a Test Case?

Jamal Raiyn, Anwar Rayan

Abstract

Homology modelling is utilized to predict the 3-D structure of a given protein (target) based on its sequence alignment to a protein whose structure (template) has been experimentally determined. The use of such technique is already rewarding and increasingly widespread in biological research and drug development. The accuracy of the predictions as commonly accepted is dependent on the score of target protein - template sequence identity. Given the sequence identity score of pairs of proteins, certain questions are raised as to whether we can assess or quantitate the quality of the obtained model. Also, whether we should choose, the protein with the highest sequence identity as a template. The answer to these questions is critical since only with such determinations, we could decide how to choose the template and to which usage the model is reliable. We intend in the paper to assess the accuracy of sequence identity-based homology modeling by analyzing a database of 4560 pair-wise sequence and structural alignments. The decision making process regarding to which parts of the known protein to perform structural alignment is not trivial and clearer rules should be extracted.

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Paper Citation


in Harvard Style

Raiyn J. and Rayan A. (2009). HOW MUCH SEQUENCE IDENTITY GUARANTEE GOOD MODELS IN HOMOLOGY MODELING - Proteins from Serine Protease Family as a Test Case? . In Proceedings of the International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2009) ISBN 978-989-8111-65-4, pages 455-458. DOI: 10.5220/0001379204550458


in Bibtex Style

@conference{biosignals09,
author={Jamal Raiyn and Anwar Rayan},
title={HOW MUCH SEQUENCE IDENTITY GUARANTEE GOOD MODELS IN HOMOLOGY MODELING - Proteins from Serine Protease Family as a Test Case?},
booktitle={Proceedings of the International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2009)},
year={2009},
pages={455-458},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0001379204550458},
isbn={978-989-8111-65-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2009)
TI - HOW MUCH SEQUENCE IDENTITY GUARANTEE GOOD MODELS IN HOMOLOGY MODELING - Proteins from Serine Protease Family as a Test Case?
SN - 978-989-8111-65-4
AU - Raiyn J.
AU - Rayan A.
PY - 2009
SP - 455
EP - 458
DO - 10.5220/0001379204550458