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ISSN:
1798-2340 (Online)
Frequency:
Monthly
DOI:
10.12720/jait
Indexing:
ESCI (Web of Science)
,
Scopus
,
CNKI
,
etc
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Acceptance Rate:
19%
APC:
500 USD
Average Days to Accept:
135 days
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Impact Factor 2022: 1.0
3.1
2022
CiteScore
49th percentile
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Editor-in-Chief
Prof. Kin C. Yow
University of Regina, Saskatchewan, Canada
I'm delighted to serve as the Editor-in-Chief of
Journal of Advances in Information Technology
.
JAIT
is intended to reflect new directions of research and report latest advances in information technology. I will do my best to increase the prestige of the journal.
What's New
2024-03-28
Vol. 15, No. 3 has been published online!
2024-02-26
The papers published in Vol. 15, Nos. 1&2 have been registered with Crossref.
2024-02-26
Vol. 15, No. 2 has been published online!
Home
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2019
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Volume 10, No. 4, November 2019
>
Clustering of Protein Conformations Using Parallelized Dimensionality Reduction
Arpita Joshi and Nurit Haspel
Dept. of Computer Science, University of Massachusetts, Boston, USA
Abstract
—Ascertaining the conformational landscape of a macromolecule, like protein is indispensable to understanding its characteristics and functions. In this work, an amassment of these techniques is presented, that would be an aid in sampling of these conformations better and faster. The datasets that represent these conformational dynamics of proteins are complex and high dimensional. Therefore, there arises a need for dimensionality reduction methods that best conserve the variance and further the analysis of the data. We present a parallelized version of a well-known dimensionality reduction method, Isomap. Isomap has been shown to produce better results than linear dimensionality reduction in approximating the complex landscape of protein folding. However, the algorithm is compute-intensive for large proteins or a large number of samples, used to model a path that a protein undergoes. We present an algorithm, parallelized using OpenMP, with a speed-up of approximately twice. The results are in agreement with the ones obtained using sequential Isomap.
Index Terms
—dimensionality reduction, Isomap, OpenMP
Cite: Arpita Joshi and Nurit Haspel, "Clustering of Protein Conformations Using Parallelized Dimensionality Reduction," Journal of Advances in Information Technology, Vol. 10, No. 4, pp. 142-147, November 2019. doi: 10.12720/jait.10.4.142-147
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