Simulation-based data mining solution to the structure of water surrounding proteins

Authors:
Hieu Chi Dam;Tu Bao Ho;Ayumu Sugiyama
Affiliations:
School of Knowledge Science, Japan Advanced Institute of Science and Technology, Japan and University of Science, Vietnam National University at Ha Noi, Vietnam and ERATO, Japan Science and Techno ...;School of Knowledge Science, Japan Advanced Institute of Science and Technology, Japan and John von Neumann Institute, Vietnam National University at Ho Chi Minh City, Vietnam;School of Knowledge Science, Japan Advanced Institute of Science and Technology, Japan and ERATO, Japan Science and Technology Agency, Japan
Venue:
IJCAI'11 Proceedings of the Twenty-Second international joint conference on Artificial Intelligence - Volume Volume Three
Year:
2011

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Abstract

What is structure of water surrounding proteins remains as one of fundamental unsolved problems of science. Methods in biophysics only provide qualitative description of the structure and thus clarifying the collective phenomena of a huge number of water molecules is still beyond intuition in biophysics. We introduce a simulation-based data mining approach that quantitatively model the structure of water surrounding a protein as clusters of water molecules having similar moving behavior. The paper presents and explains how the advances of AI technique can potentially solve this challenging data-intensive problem.