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Normal Mode Analysis as a Routine Part of a Structural Investigation [PDF]
Molecules, 2019 Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance.
Jacob A. Bauer +2 more
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Normal mode analysis and beyond [PDF]
Biophysics and Physicobiology, 2019 Normal mode analysis provides a powerful tool in biophysical computations. Particularly, we shed light on its application to protein properties because they directly lead to biological functions. As a result of normal mode analysis, the protein motion is
Takahisa Yamato, Olivier Laprévote
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Normal mode analysis in multi-coupled non-Hermitian optical nanocavities [PDF]
Scientific Reports, 2023 Coupled optical cavities are an attractive on-chip optical platform for realizing quantum mechanical concepts in electrodynamics and further developing non-Hermitian photonics.
Kyong-Tae Park +3 more
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Interpretation of Single-Molecule Force Experiments on Proteins Using Normal Mode Analysis [PDF]
Nanomaterials, 2021 Single-molecule force spectroscopy experiments allow protein folding and unfolding to be explored using mechanical force. Probably the most informative technique for interpreting the results of these experiments at the structural level makes use of ...
Jacob Bauer, Gabriel Žoldák
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HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes [PDF]
Frontiers in Molecular Biosciences, 2021 Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in their native environment (in situ). Its potential of providing information on the dynamics of macromolecular complexes in cells is still largely unexploited, due ...
Mohamad Harastani +3 more
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Vibrational effects on polarizability: insights from normal mode analysis [PDF]
Scientific ReportsThe performance of sensing and optical devices is closely linked to the molecular polarizability response, a property significantly influenced by the polarizability tensor’s isotropic and anisotropic components.
Tiago de Sousa Araújo Cassiano +3 more
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Normal mode analysis of a relaxation process with Bayesian inference [PDF]
Science and Technology of Advanced Materials, 2020 Measurements of relaxation processes are essential in many fields, including nonlinear optics. Relaxation processes provide many insights into atomic/molecular structures and the kinetics and mechanisms of chemical reactions.
Itsushi Sakata +6 more
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fSUB: normal mode analysis with flexible substructures. [PDF]
J Phys Chem B, 2012 In this paper, we report a novel normal-mode analysis for supramolecular complexes, named fSUB. The method models a complex as a group of flexible substructures. The low-frequency substructure modes are first determined with substructures in isolation, and the motions of the whole complex are then calculated on the basis of substructure modes and ...
Lu M, Ming D, Ma J.
europepmc +4 more sources
Hybrid Electron Microscopy Normal Mode Analysis with Scipion. [PDF]
Protein Sci, 2020 AbstractHybrid Electron Microscopy Normal Mode Analysis (HEMNMA) method was introduced in 2014. HEMNMA computes normal modes of a reference model (an atomic structure or an electron microscopy map) of a molecular complex and uses this model and its normal modes to analyze single‐particle images of the complex to obtain information on its continuous ...
Harastani M, Sorzano COS, Jonić S.
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iMODS: internal coordinates normal mode analysis server. [PDF]
Nucleic Acids Res, 2014 Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules.
López-Blanco JR +3 more
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