MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing

  • Natalie E. Castellana
  • Andrey Lushnikov
  • Piotr Rotkiewicz
  • Natasha Sefcovic
  • Pavel A. Pevzner
  • Adam Godzik
  • Kira Vyatkina
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7534)

Abstract

Proteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein function. At the same time, experimental techniques provide us with only single snapshots of the whole ensemble of available conformations. Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations. We present a novel, efficient morphing algorithm, Morph-Pro based on linear interpolation. We also show that apart from visualization, morphing can be used to provide plausible intermediate structures. We test intermediate structures constructed by our algorithm for a protein kinase and evaluate these structures in a virtual docking experiment. The structures are shown to dock with higher score to known ligands than structures solved using X-Ray crystallography.

Keywords

protein morphing virtual docking 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Natalie E. Castellana
    • 1
  • Andrey Lushnikov
    • 4
  • Piotr Rotkiewicz
    • 2
  • Natasha Sefcovic
    • 3
  • Pavel A. Pevzner
    • 1
  • Adam Godzik
    • 2
  • Kira Vyatkina
    • 4
  1. 1.Department of Computer ScienceUniversity of California-San DiegoUSA
  2. 2.Burnham Institute for Medical ResearchLa JollaUSA
  3. 3.Joint Center for Structural Genomics, Bioinformatics CoreUniversity of California-San DiegoUSA
  4. 4.Algorithmic Biology LaboratorySaint Petersburg Academic UniversitySaint PetersburgRussia

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