Forum 09/11/2003

“NMFF: Flexible fitting of atomic structures into low-resolution EM maps using elastic network normal mode analysis”

Florence Tama – Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA

We present a novel moethod for the quantitative flexible docking of a high-resolution structure into low-resolution maps of macromolecular complexes from electron microscopy. This method uses a linear combination of low frequency normal modes from elastic network in an iterative manner to deform the structure optimally to conform to the low-resolution electron density map. We demonstrate that refinement based on normal mode analysis provides an accurate and fast alternative for the flexible fitting of high-resolution structure into low-resolution density map determined by electron microscopy. Additionally, we show that lower resolution (multi-scale) structural models can also be used for the normal mode searching in lieu of fully atomic models with little loss of overall accuracy.