Journal
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
Volume 28, Issue 9, Pages 3126-3137Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TVCG.2021.3051632
Keywords
Distribution functions; Trajectory; Visualization; Graphical models; Numerical models; Shape; Periodic structures; Molecule visualization; molecular dynamics; interactive exploration
Categories
Funding
- Excellence Center at Linkoping and Lund in Information Technology (ELLIIT)
- Swedish e-Science Research Centre (SeRC)
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Spatial distribution functions (SDF) are fundamental instruments in molecular analysis for understanding the spatial occurrences and relations of atomic structures over time. This study introduces the concept of an internal frame of reference (IFR) and proposes an algorithm to track the IFR over time and space. The usefulness of this technique is demonstrated through its application to temporal molecular trajectories and ensemble datasets.
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 Kabsch's 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.
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