An Approach for Clustering Protein Pockets into Similar Groups
(0) Abstract In this work, we propose a network-based approach to cluster the protein pockets into similar groups in a database level. A pocket similarity network is constructed to describe structural similarity relationships among the pockets from the systematic perspective, which possesses the community structures and can can be utilized to develop a direct method to cluster the pockets by partitioning the network to small communities, which correspond to pocket groups individually. As a first step, we join the pockets into structurally similar pocket groups via a hierarchical process guided by maximizing a widely used modularity measurement Q. Then we analyze the functional similarity underlying every divided pocket groups. As a result most of the pockets in the same group are identified to share similar functions. These results show that our clustering method is effective and efficient to reveal biologically meaningful pocket groups regard to functional consistence.
Keywords Protein pockets clustering pockets similarity network functional genomics systems biology.
Zhi-Ping Liu Ling-Yun Wu Yong Wang Xiang-Sun Zhang Luonan Chen
Institute of Applied Mathematics, Academy of Mathematics and Systems Science Chinese Academy of Scie Institute of Applied Mathematics, Academy of Mathematics and Systems Science Chinese Academy of Scie Department of Electronics, Information and Communication Engineering Osaka Sangyo University, Osaka
国际会议
首届伏化合系统生物学国际会议(The First International Symposium OSB07)
北京
英文
204-212
2007-08-08（万方平台首次上网日期，不代表论文的发表时间）