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Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions

Authors
  • Skånberg, Robin
  • Falk, Martin
  • Linares, Mathieu
  • Ynnerman, Anders
  • Hotz, Ingrid
Publication Date
Jan 01, 2021
Identifiers
DOI: 10.1109/TVCG.2021.3051632
OAI: oai:DiVA.org:liu-174336
Source
DiVA - Academic Archive On-line
Keywords
Language
English
License
Green
External links

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. / <p>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.</p>

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