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Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models

  • Sumudu P. Leelananda
  • Robert L. Jernigan
  • Andrzej KloczkowskiEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)

Abstract

Highly designable structures can be distinguished based on certain geometric graphical features of the interactions confirming the fact that the topology of a protein structure and its residue-residue interaction network are important determinants of its designability. The most designable structures and poorly designable structures obtained for sets of proteins having the same number of residues are compared, and it is shown that the most designable structures predicted by the graph features of the contact diagrams are more densely packed whereas the poorly designable structures are more open loop type structures or structures that are loosely packed. Interestingly enough, it can also be seen that these highly designable structures obtained are also common structural motifs found in nature.

Keywords

Designability Contact maps Graph features 

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Sumudu P. Leelananda
    • 4
  • Robert L. Jernigan
    • 1
    • 2
  • Andrzej Kloczkowski
    • 3
    • 4
    Email author
  1. 1.Iowa State UniversityAmesUSA
  2. 2.Baker Center for Bioinformatics and Biological StatisticsAmesUSA
  3. 3.The Ohio State UniversityColumbusUSA
  4. 4.Nationwide Children’s HospitalColumbusUSA

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