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A Filtering Technique for Fragment Assembly- Based Proteins Loop Modeling with Constraints

  • Federico Campeotto
  • Alessandro Dal Palù
  • Agostino Dovier
  • Ferdinando Fioretto
  • Enrico Pontelli
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7514)

Abstract

Methods to predict the structure of a protein often rely on the knowledge of macro sub-structures and their exact or approximated relative positions in space. The parts connecting these sub-structures are called loops and, in general, they are characterized by a high degree of freedom. The modeling of loops is a critical problem in predicting protein conformations that are biologically realistic. This paper introduces a class of constraints that models a general multi-body system; we present a proof of NP-completeness and provide filtering techniques, inspired by inverse kinematics, that can drastically reduce the search space of potential conformations. The paper shows the application of the constraint in solving the protein loop modeling problem, based on fragments assembly.

Keywords

Rigid Body Root Mean Square Deviation Loop Modeling Protein Structure Prediction Rigid Block 
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 2012

Authors and Affiliations

  • Federico Campeotto
    • 1
    • 2
  • Alessandro Dal Palù
    • 3
  • Agostino Dovier
    • 2
  • Ferdinando Fioretto
    • 1
  • Enrico Pontelli
    • 1
  1. 1.Dept. Computer ScienceNew Mexico State UniversityUSA
  2. 2.Depts. Math. & Computer ScienceUniversity of UdineItaly
  3. 3.Dept. MathematicsUniversity of ParmaItaly

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