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Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices
Article first published online: 20 APR 2007
DOI: 10.1002/jcc.20700
Copyright © 2007 Wiley Periodicals, Inc.
1096-987X/asset/cover.gif?v=1&s=4429aac2462ebd499c13b3d7fe983679c5767778 "Journal of Computational Chemistry")
Additional Information
How to Cite
González-Díaz, H., Pérez-castillo, Y., Podda, G. and Uriarte, E. (2007), Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices. Journal of Computational Chemistry, 28: 1990–1995. doi: 10.1002/jcc.20700
Publication History
- Issue published online: 22 JUN 2007
- Article first published online: 20 APR 2007
- Manuscript Accepted: 19 JAN 2007
- Manuscript Received: 15 DEC 2006
Funded by
- Dipartimento Farmaco Chimico Tecnologico of the University of Cagliari
- Ministerio de Sanidad y Consumo. Grant Numbers: PXIB20304PR, BTF20302PR, PI061457
Keywords:
- protein structure;
- topological indices;
- spectral moments;
- protein stability
Graphical Abstract
Abstract
In principle, there are different protein structural parameters that can be used in computational chemistry studies to classify protein mutants according to thermal stability including: sequence, connectivity, and 3D descriptors. Connectivity parameters (called topological indices, TIs) are simpler than 3D parameters being then less computationally expensive. However, TIs ignore important aspects of protein structure and hence are expected to be inaccurate. In any case, a comparison of 3D and TIs has not been reported with respect to the power of discrimination of proteins according to stability. In this study, we compare both classes of indices in this sense by the first time. The best model found, based on 3D spectral moments correctly classified 507 out of 525 (96.6%) proteins while TIs model correctly classified 404 out of 525 (77.0%) proteins. We have shown that, in fact, 3D descriptor models gave more accurate results than TIs but interestingly, TIs give acceptable results in a timely way in spite of their simplicity. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007