title: iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates.
abstract: Here, we employed the collective motions extracted from Normal Mode Analysis (NMA) in internal coordinates (torsional space) for the flexible fitting of atomic-resolution structures into electron microscopy (EM) density maps. The proposed methodology was validated using a benchmark of simulated cases, highlighting its robustness over the full range of EM resolutions and even over coarse-grained representations. A systematic comparison with other methods further showcased the advantages of this proposed methodology, especially at medium to lower resolutions. Using this method, computational costs and potential overfitting problems are naturally reduced by constraining the search in low-frequency NMA space, where covalent geometry is implicitly maintained. This method also effectively captures the macromolecular changes of a representative set of experimental test cases. We believe that this novel approach will extend the currently available EM hybrid methods to the atomic-level interpretation of large conformational changes and their functional implications.
authors.affiliation: Department of Biological Physical Chemistry, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain.
authors.forename: José Ramón
authors.initials: JR
authors.lastname: Lopéz-Blanco
authors.forename: Pablo
authors.initials: P
authors.lastname: Chacón
mesh_terms: D000465:Algorithms; D018834:Chaperonin 60 / Q000737:chemistry / Q000648:ultrastructure; D003198:Computer Simulation; D020285:Cryoelectron Microscopy; D003627:Data Interpretation, Statistical; D008870:Microtubules / Q000737:chemistry / Q000648:ultrastructure; D008958:Models, Molecular; D020836:Protein Structure, Quaternary; D012270:Ribosomes / Q000737:chemistry / Q000648:ultrastructure; D012984:Software
chemical_list: D018834:Chaperonin 60
keywords: Coarse-grained models; Flexible fitting; Hybrid methods; Internal coordinates; Molecular modeling; Normal mode analysis