Folding-aware and Structure-conscious 3D Substructures in Folding Data: Identification and Applications

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外文摘要：Molecular dynamics simulations have been employed by biologists to study the protein folding problem。 Such simulations have resulted in a large number of protein folding trajectories， each of which consists of a sequence of three-dimensional conformations。 Existing analysis typically represents a 3D conformation as a scalar variable such as radius of gyration。 Although more recent studies have looked into more substructure-centered representations， they however do not take the folding properties into account。 In this article， we propose the concept of folding-aware， structure-conscious (FASC) substructures。 We propose a 3-step algorithm to extract such FASC substructures。 We have also applied these substructures to address three important applications， including identification of structurally similar 3D conformations， conformational space segmentation， and cross-trajectory comparison。

外文关键词：

protein folding trajectories3D substructure identificationstructure-based similarity analysiscross-trajectory comparison

作者：

Hui Yang、Saurabh Gupte、Runtang Wang、Rahul Parte

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作者单位：

Dept of Computer Science San Francisco State Univ. San Francisco, CA, 94132

会议名称：

International conference on bioinformatics and computational biology;BICoB-2010

会议地点：

Honolulu, HI(US);Honolulu, HI(US)

会议母体文献：

2nd international conference on bioinformatics and computational biology 2010

页码：

P.145-150

出版时间：

2010