Algorithm for normal mode analysis with general internal coordinates

2003 ◽  
Vol 24 (7) ◽  
pp. 826-841 ◽  
Author(s):  
Kenshu Kamiya ◽  
Yoko Sugawara ◽  
Hideaki Umeyama
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
General Internal ◽  
Internal Coordinates

scholarly journals iMod: multipurpose normal mode analysis in internal coordinates

2011 ◽  
Vol 27 (20) ◽  
pp. 2843-2850 ◽  
Author(s):  
José Ramón Lopéz-Blanco ◽  
José Ignacio Garzón ◽  
Pablo Chacón
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Internal Coordinates

scholarly journals Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal coordinates

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0258818
Author(s):  
Byung Ho Lee ◽  
Soon Woo Park ◽  
Soojin Jo ◽  
Moon Ki Kim
Keyword(s):  
Normal Mode ◽  
Conformational Changes ◽  
Degrees Of Freedom ◽  
Large Scale ◽  
Conformational Transition ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Theoretical Approaches ◽  
Internal Coordinates ◽  
Transition Pathways

Large-scale conformational changes are essential for proteins to function properly. Given that these transition events rarely occur, however, it is challenging to comprehend their underlying mechanisms through experimental and theoretical approaches. In this study, we propose a new computational methodology called internal coordinate normal mode-guided elastic network interpolation (ICONGENI) to predict conformational transition pathways in proteins. Its basic approach is to sample intermediate conformations by interpolating the interatomic distance between two end-point conformations with the degrees of freedom constrained by the low-frequency dynamics afforded by normal mode analysis in internal coordinates. For validation of ICONGENI, it is applied to proteins that undergo open-closed transitions, and the simulation results (i.e., simulated transition pathways) are compared with those of another technique, to demonstrate that ICONGENI can explore highly reliable pathways in terms of thermal and chemical stability. Furthermore, we generate an ensemble of transition pathways through ICONGENI and investigate the possibility of using this method to reveal the transition mechanisms even when there are unknown metastable states on rough energy landscapes.

scholarly journals Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis

2016 ◽  
Vol 24 (20) ◽  
pp. 4855-4866 ◽  
Author(s):  
Victor A. Gil ◽  
Daniel Lecina ◽  
Christoph Grebner ◽  
Victor Guallar
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Internal Coordinates

scholarly journals Modeling Macromolecular Flexibility with Normal Mode Analysis in Internal Coordinates

2012 ◽  
Vol 102 (3) ◽  
pp. 394a
Author(s):  
Jose Ramon Lopez-Blanco ◽  
Erney Ramirez-Aportela ◽  
Santiago Garcia-Sanchez ◽  
Pieter Chys ◽  
Pablo Chacon
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Internal Coordinates

scholarly journals iMODS: internal coordinates normal mode analysis server

2014 ◽  
Vol 42 (W1) ◽  
pp. W271-W276 ◽  
Author(s):  
José Ramón López-Blanco ◽  
José I. Aliaga ◽  
Enrique S. Quintana-Ortí ◽  
Pablo Chacón
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Internal Coordinates

scholarly journals Intramolecular hydrogen bond: Can it be part of the basis set of valence internal coordinates in normal mode analysis?

2015 ◽  
Vol 127 (6) ◽  
pp. 1127-1134 ◽  
Author(s):  
SARVESH KUMAR PANDEY ◽  
PRASANTA DAS ◽  
PUSPENDU K DAS ◽  
ELANGANNAN ARUNAN ◽  
SADASIVAM MANOGARAN
Keyword(s):  
Hydrogen Bond ◽  
Normal Mode ◽  
Intramolecular Hydrogen Bond ◽  
Normal Mode Analysis ◽  
Basis Set ◽  
Mode Analysis ◽  
Internal Coordinates ◽  
Intramolecular Hydrogen

RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  
Keyword(s):  
Force Constant ◽  
Raman Spectra ◽  
Normal Mode ◽  
Raman Band ◽  
Normal Mode Analysis ◽  
Force Constants ◽  
Mode Analysis ◽  
Oxidation Number

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.

scholarly journals Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer

2020 ◽  
Vol 153 (21) ◽  
pp. 215103
Author(s):  
Alexander Klinger ◽  
Dominik Lindorfer ◽  
Frank Müh ◽  
Thomas Renger
Keyword(s):  
Energy Transfer ◽  
Spectral Density ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis

scholarly journals Normal-mode analysis for scalar fields in BTZ black-hole background

2009 ◽  
Vol 60 (2) ◽  
pp. 169-173 ◽  
Author(s):  
Sayan K. Chakrabarti ◽  
Pulak Ranjan Giri ◽  
Kumar S. Gupta
Keyword(s):  
Black Hole ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Scalar Fields ◽  
Mode Analysis ◽  
Btz Black Hole ◽  
Black Hole Background
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