title: The subspace iteration method in protein normal mode analysis.
abstract: Normal mode analysis plays an important role in relating the conformational dynamics of proteins to their biological function. The subspace iteration method is a numerical procedure for normal mode analysis that has enjoyed widespread success in the structural mechanics community due to its numerical stability and computational efficiency in calculating the lowest normal modes of large systems. Here, we apply the subspace iteration method to proteins to demonstrate its advantageous properties in this area of computational protein science. An effective algorithm for choosing the number of iteration vectors in the method is established, offering a considerable improvement over the original implementation. In the present application, computational time scales linearly with the number of normal modes computed. Additionally, the method lends itself naturally to normal mode analyses of multiple neighboring macromolecular conformations, as demonstrated in a conformational change pathway analysis of adenylate kinase. These properties, together with its computational robustness and intrinsic scalability to multiple processors, render the subspace iteration method an effective and reliable computational approach to protein normal mode analysis.
authors.affiliation: Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Reza Sharifi
authors.initials: RS
authors.lastname: Sedeh
authors.forename: Mark
authors.initials: M
authors.lastname: Bathe
authors.forename: Klaus-Jürgen
authors.initials: KJ
authors.lastname: Bathe
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D009716:Numerical Analysis, Computer-Assisted; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins