title: Generating conformational transitions using the euclidean distance matrix.
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.
authors.forename: Xiao-Bo
authors.initials: XB
authors.lastname: Li
authors.forename: Forbes
authors.initials: F
authors.lastname: Burkowski
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding