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2010
Springer

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

10 years 9 months ago
Folding-aware and Structure-conscious 3D Substructures in Folding Data: Identification and Applications
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. Key Words: protein folding trajectories, 3D substructure identification, structure-based similarity a...
Hui Yang, Saurabh Gupte, Runtang Wang, Rahul Parte
Added 18 Jul 2010
Updated 18 Jul 2010
Type Conference
Year 2010
Where BICOB
Authors Hui Yang, Saurabh Gupte, Runtang Wang, Rahul Parte
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