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...

• Type: Conference
• Year: 2010
• Where: BICOB
• Authors: Hui Yang, Saurabh Gupte, Runtang Wang, Rahul Parte
• Keywords: BICOB 2010, Computational Biology, Protein Folding, Protein Folding Problem, Protein Folding Trajectories