Journal Articles Journal of Computational Chemistry Year : 2014

Rapid determination of RMSDs corresponding to macromolecular rigid body motions

Abstract

Finding the root mean sum of squared deviations (RMSDs) between two coordinate vectors that correspond to the rigid body motion of a macromolecule is an important problem in structural bioinformatics, computational chemistry, and molecular modeling. Standard algorithms compute the RMSD with time proportional to the number of atoms in the molecule. Here, we present RigidRMSD, a new algorithm that determines a set of RMSDs corresponding to a set of rigid body motions of a macromolecule in constant time with respect to the number of atoms in the molecule. Our algorithm is particularly useful for rigid body modeling applications, such as rigid body docking, and also for high-throughput analysis of rigid body modeling and simulation results. We also introduce a constant-time rotation RMSD as a similarity measure for rigid molecules. A C++ implementation of our algorithm is available at http://nano-d.inrialpes.fr/software/RigidRMSD.
Fichier principal
Vignette du fichier
JCC_RMSD_final.pdf (292) Télécharger le fichier
RMSD_SI.pdf (84) Télécharger le fichier
Origin Files produced by the author(s)
Format Other

Dates and versions

hal-00952248 , version 1 (26-02-2014)

Identifiers

Cite

Petr Popov, Sergei Grudinin. Rapid determination of RMSDs corresponding to macromolecular rigid body motions. Journal of Computational Chemistry, 2014, 35 (12), pp.950-956. ⟨10.1002/jcc.23569⟩. ⟨hal-00952248⟩
387 View
883 Download

Altmetric

Share

More