Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to…

• FD
  Fundação de Amparo à Pesquisa do Estado de São Paulo

  Awards: 2010/16947-9, 2013/05475-7, 2011/51348-1
• CN
  Conselho Nacional de Desenvolvimento Científico e Tecnológico

  Awards: -0 and, 470374/2013-6, 2013-0, 304058/2013-0
• UE
  Universidade Estadual de Campinas