Journalartikel

Jahr der Veröffentlichung: 2016

Seiten: 1423-1434

Zeitschrift: IEEE Transactions on Knowledge and Data Engineering

Bandnummer: 28

Heftnummer: 6

ISSN: 1041-4347

eISSN: 1558-2191

DOI Link: https://doi.org/10.1109/TKDE.2016.2520484

Verlag: Institute of Electrical and Electronics Engineers

Abstract: 
CavBase is a database containing information about the three-dimensional geometry and the physicochemical properties of putative protein binding sites. Analyzing CavBase data typically involves computing the similarity of pairs of binding sites. In contrast to sequence alignment, however, a structural comparison of protein binding sites is a computationally challenging problem, making large scale studies difficult or even infeasible. One possibility to overcome this obstacle is to precompute pairwise similarities in an all-against-all comparison, and to make these similarities subsequently accessible to data analysis methods. Pairwise similarities, once being computed, can also be used to equip CavBase with a neighborhood structure. Taking advantage of this structure, methods for problems such as similarity retrieval can be implemented efficiently. In this paper, we tackle the problem of performing an all-against-all comparison using CavBase, consisting of more than 200,000 protein cavities, by means of parallel computation and cloud computing techniques. We present the conceptual design and technical realization of a large-scale study to create a similarity database called CavSimBase. We illustrate how CavSimBase is constructed, is accessed, and is used to answer biological questions by data analysis and similarity retrieval.

Harvard-Zitierstil: Leinweber, M., Fober, T., Strickert, M., Baumgaertner, L., Klebe, G., Freisleben, B., et al. (2016) CavSimBase: A Database for Large Scale Comparison of Protein Binding Sites, IEEE Transactions on Knowledge and Data Engineering, 28(6), pp. 1423-1434. https://doi.org/10.1109/TKDE.2016.2520484

APA-Zitierstil: Leinweber, M., Fober, T., Strickert, M., Baumgaertner, L., Klebe, G., Freisleben, B., & Huellermeier, E. (2016). CavSimBase: A Database for Large Scale Comparison of Protein Binding Sites. IEEE Transactions on Knowledge and Data Engineering. 28(6), 1423-1434. https://doi.org/10.1109/TKDE.2016.2520484