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On the Convergence of Protein Structure and Dynamics. Statistical Learning Studies of Pseudo Folding Pathways

  • Alessandro Vullo
  • Andrea Passerini
  • Paolo Frasconi
  • Fabrizio Costa
  • Gianluca Pollastri
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4973)

Abstract

Many algorithms that attempt to predict proteins’ native structure from sequence need to generate a large set of hypotheses in order to ensure that nearly correct structures are included, leading to the problem of assessing the quality of alternative 3D conformations. This problem has been mostly approached by focusing on the final 3D conformation, with machine learning techniques playing a leading role. We argue in this paper that additional information for recognising native-like structures can be obtained by regarding the final conformation as the result of a generative process reminiscent of the folding process that generates structures in nature. We introduce a coarse representation of protein pseudo-folding based on binary trees and introduce a kernel function for assessing their similarity. Kernel-based analysis techniques empirically demonstrate a significant correlation between information contained into pseudo-folding trees and features of native folds in a large and non-redundant set of proteins.

Keywords

Binary Tree Conformational Space Protein Structure Prediction Folding Process Folding Pathway 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Alessandro Vullo
    • 1
  • Andrea Passerini
    • 2
  • Paolo Frasconi
    • 2
  • Fabrizio Costa
    • 2
  • Gianluca Pollastri
    • 1
  1. 1.School of Computer Science and InformaticsUniversity College DublinDublin 4Ireland
  2. 2.Dipartimento di Sistemi e InformaticaUniversità degli Studi di FirenzeFirenzeItaly

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