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Keywords:

  • RMSD calculation;
  • rigid body motion;
  • quaternion arithmetic;
  • structure comparison;
  • rigid body clustering

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. © 2014 Wiley Periodicals, Inc.