Title :
Generating Conformational Transitions Using the Euclidean Distance Matrix
Author :
Xiao-Bo Li ; Burkowski, Forbes
Author_Institution :
Cheriton Sch. of Comput. Sci., Univ. of Waterloo, Waterloo, ON, Canada
Abstract :
Elastic network interpolation (ENI) is an efficient method for generating intermediate conformations between two end protein conformations. Its current formulation uses interatomic distance. We show how this can be generalized to interatomic distances-squared. This generalization is part of an effort to study protein dynamics on the set of positive semidefinite (PSD) matrices, which has a rich mathematical structure. We use lattice structures to test this interpolation scheme, and discuss some limitations observed. We conclude with some suggestions for future research.
Keywords :
bond lengths; interpolation; molecular biophysics; molecular configurations; proteins; ENI; Euclidean distance matrix; PSD; conformational transitions; elastic network interpolation; interatomic distance-squared; intermediate conformations; lattice structures; mathematical structure; positive semidefinite matrices; protein conformations; protein dynamics; Equations; Interpolation; Manifolds; Mathematical model; Nanobioscience; Proteins; Yttrium; Conformational transitions; Euclidean distance matrices; Riemannian manifold; positive semidefinite matrices;
Journal_Title :
NanoBioscience, IEEE Transactions on
DOI :
10.1109/TNB.2014.2387156
