Space Constrained Homology Modelling : The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus
Joint Authors
Kossida, Sophia
Kontopoulos, Dimitrios Georgios
Vlachakis, Dimitrios
Source
Computational and Mathematical Methods in Medicine
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-08-06
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
Protein structure is more conserved than sequence in nature.
In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape.
Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus.
The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp.
The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure.
The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling.
Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures.
American Psychological Association (APA)
Vlachakis, Dimitrios& Kontopoulos, Dimitrios Georgios& Kossida, Sophia. 2013. Space Constrained Homology Modelling : The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus. Computational and Mathematical Methods in Medicine،Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-447104
Modern Language Association (MLA)
Vlachakis, Dimitrios…[et al.]. Space Constrained Homology Modelling : The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus. Computational and Mathematical Methods in Medicine No. 2013 (2013), pp.1-9.
https://search.emarefa.net/detail/BIM-447104
American Medical Association (AMA)
Vlachakis, Dimitrios& Kontopoulos, Dimitrios Georgios& Kossida, Sophia. Space Constrained Homology Modelling : The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus. Computational and Mathematical Methods in Medicine. 2013. Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-447104
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-447104