Section: New Software and Platforms

RigidRMSD

A library for rapid computations of the root mean square deviations (RMSDs) corresponding to a set of rigid body transformations of a coordinate vector

Keyword: Bioinformatics

Functional Description: RigidRMSD is a library for rapid computations of the root mean square deviations (RMSDs) corresponding to a set of rigid body transformations of a coordinate vector (which can be a molecule in PDB format, for example). Calculation of the RMSD splits into two steps:

Initialization, which is linear in the number of vector entities (or particles in a rigid body). RMSD computation, which is computed in constant time for a single rigid-body spatial transformation (rotation + translation). This step uses the inertia tensor and the the center of mass computed on the first step. Initialization step is performed only once. It makes RigidRMSD particularly useful when computing multiple RMSDs, since each new RMSD calculation takes only constant time.

• Participants: Petr Popov and Sergey Grudinin

• Contact: Sergey Grudinin

• Publication: Rapid determination of RMSDs corresponding to macromolecular rigid body motions

• URL: https://team.inria.fr/nano-d/software/rigidrmsd/