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In bioinformatics, the root mean square deviation of atomic positions, or simply root mean square deviation (RMSD), is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed molecules. [1]
In bioinformatics, the root mean square deviation of atomic positions is the measure of the average distance between the atoms of superimposed proteins. In structure based drug design , the RMSD is a measure of the difference between a crystal conformation of the ligand conformation and a docking prediction.
Another method to describe the motion of a Brownian particle was described by Langevin, now known for its namesake as the Langevin equation.) (,) = (,), given the initial condition (, =) = (); where () is the position of the particle at some given time, is the tagged particle's initial position, and is the diffusion constant with the S.I. units ...
The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.
It could be used to infer the evolutionary relationship among a set of proteins even with low sequence similarity. Structural alignment implies superimposing a 3D structure over a second one, rotating and translating atoms in corresponding positions (in general, using the C α atoms or even the backbone heavy atoms C, N, O, and C α).
Examples of correlation between RCI and other methods of measuring motional amplitudes in proteins. NMR RMSD - root mean square fluctuations of atomic coordinates in NMR ensembles, MD RMSD - root mean square fluctuations of atomic coordinates in MD ensembles, S2 - model-free order parameter, RCI - random coil index, B-factor - temperature factor of X-ray structures; RCI->NMR RMSD - root mean ...
But I guess it would be OK to wikilink from Molecular dynamics to a subsection on RMSD in Structural alignment. Olli Niemitalo 07:28, 30 August 2013 (UTC) Another option is to move to "Root-mean-square deviation of atomic positions" for now, no extra effort required. Will do that. Olli Niemitalo 06:58, 1 September 2013 (UTC)
Swap — Atomic coordinate swapping for improved RMSD alignment; Intervor — Protein-Protein interface extraction and display; SurfVol — Measure surface area and volume of proteins [16] vmdICE — Plugin for computing RMSD, RMSF, SASA, and other time-varying quantities [17]