Fast alignment and comparison of RNA structures

Link:
Autor/in:
Erscheinungsjahr:
2013
Medientyp:
Text
Schlagworte:
  • Proteins
  • Structure (composition)
  • Structural alignment
  • Molecular Dynamics Simulation
  • Molecular Dynamics
  • Proteins
  • Structure (composition)
  • Structural alignment
  • Molecular Dynamics Simulation
  • Molecular Dynamics
Beschreibung:
  • Motivation: To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift {[}O(n(2))], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, which are characterized by their memberships in a probabilistic classification based on local geometry and H-bonding descriptors. This leads to a probabilistic similarity measure that is used in a conventional dynamic programming method. Results: Examples are given of database searching, the detection of structural similarities, which would not be found using sequence based methods, and comparisons with a previously published approach.
Lizenz:
  • info:eu-repo/semantics/openAccess
Quellsystem:
Forschungsinformationssystem der UHH

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oai:www.edit.fis.uni-hamburg.de:publications/0c16a85c-f6ed-40fc-a51a-e9a92ed0929a