Rapid determination of RMSDs corresponding to macromolecular rigid body motions

Petr Popov 1 Sergei Grudinin 1, *
* Corresponding author
1 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
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.
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Contributor : Sergei Grudinin <>
Submitted on : Wednesday, February 26, 2014 - 2:10:15 PM
Last modification on : Tuesday, May 21, 2019 - 11:48:13 AM
Long-term archiving on : Monday, May 26, 2014 - 12:00:44 PM

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

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