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A Probabilistic Graphical Model for Ab Initio Folding

  • Feng Zhao
  • Jian Peng
  • Joe DeBartolo
  • Karl F. Freed
  • Tobin R. Sosnick
  • Jinbo Xu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5541)

Abstract

Despite significant progress in recent years, ab initio folding is still one of the most challenging problems in structural biology. This paper presents a probabilistic graphical model for ab initio folding, which employs Conditional Random Fields (CRFs) and directional statistics to model the relationship between the primary sequence of a protein and its three-dimensional structure. Different from the widely-used fragment assembly method and the lattice model for protein folding, our graphical model can explore protein conformations in a continuous space according to their probability. The probability of a protein conformation reflects its stability and is estimated from PSI-BLAST sequence profile and predicted secondary structure. Experimental results indicate that this new method compares favorably with the fragment assembly method and the lattice model.

Keywords

protein structure prediction ab initio folding conditional random fields (CRFs) directional statistics fragment assembly lattice model 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Feng Zhao
    • 1
  • Jian Peng
    • 1
  • Joe DeBartolo
    • 2
  • Karl F. Freed
    • 3
  • Tobin R. Sosnick
    • 2
  • Jinbo Xu
    • 1
  1. 1.Toyota Technological Institute at ChicagoChicagoUSA
  2. 2.Department of Biochemistry and Molecular Biologythe University of ChicagoChicagoUSA
  3. 3.Department of Chemistrythe University of ChicagoChicagoUSA

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