Essential dynamics of proteins

By A. Amadei, A. Linssen, H. Berendsen. 1993

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Citations in the corpus

Kinetic distance and kinetic maps from molecular dynamics simulation. (2015, background): “In order to reduce the computational cost, we can choose to keep only the eigenvectors that account for a certain fraction of the total variation in kinetic distance, as it is commonly practiced in principal component analysis [12, 2].”
Principles of Flexible Protein-Protein Docking (2008, background): “59 These degrees of freedom are described by vectors which are often called essential modes, or principal components (PC).”
Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS (2004, methodology): “While thermal equilibration typically takes 100 ps or so, in our experience conformational equilibrium may take up to 1 ns to be established for such DNA systems, and can only be confirmed retrospectively through techniques such as PCA (see below).”
A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo (1999, methodology): “[2] but using torsion angles instead of position information [28].”
Dynamics of proteins in solution (2019, result): “Furthermore, the results can be compared with much more costly computer simulations aiming for the so-called essential dynamics or proteins, i.e. a smaller set of motions that describe larger protein motions with good accuracy (Amadei et al., 1993).”
Detection of Functional Modes in Protein Dynamics (2009, methodology): “In protein simulations the first 10–20 PCs (with the largest eigenvalues) often account for a large fraction (80–90%) of the atomic MSF, and higher PCs describe smaller motions such as angle vibrations [ 10 ].”