1. Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions
- Author
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Robin Skånberg, Mathieu Linares, Ingrid Hotz, Anders Ynnerman, and Martin Falk
- Subjects
Computer and Information Sciences ,Relation (database) ,Numerical models ,Computer science ,Computation ,Periodic structures ,Trajectory ,02 engineering and technology ,Space (mathematics) ,Frame of reference ,chemistry.chemical_compound ,Computer Graphics ,0202 electrical engineering, electronic engineering, information engineering ,Point (geometry) ,Graphical model ,Visualization ,Matematik ,Spacetime ,Shape ,Data- och informationsvetenskap ,020207 software engineering ,Kemi ,DNA ,Computer Graphics and Computer-Aided Design ,chemistry ,Chemical Sciences ,Signal Processing ,Computer Vision and Pattern Recognition ,Graphical models ,Algorithm ,Distribution functions ,Mathematics ,Algorithms ,Software - Abstract
In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time. Given a molecular trajectory, SDFs can, for example, reveal the occurrence of water in relation to particular structures and hence provide clues of hydrophobic and hydrophilic regions. For the computation of meaningful distribution functions, the definition of molecular reference structures is essential. Therefore we introduce the concept of an internal frame of reference (IFR) for labeled point sets that represent selected molecular structures, and we propose an algorithm for tracking the IFR over time and space using a variant of Kabschs algorithm. This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles. We demonstrate the usefulness of the technique by applying it to temporal molecular trajectories as well as ensemble datasets. The examples include different docking scenarios with DNA, insulin, and aspirin. Funding agencies:This work was supported through grants from the ExcellenceCenter at Link¨oping and Lund in Information Technology(ELLIIT) and the Swedish e-Science Research Centre(SeRC). The authors thanks the Swedish National Infrastructurefor Computing (SNIC) for providing computingresources.
- Published
- 2022
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