Local Search Heuristic for Rigid Protein Docking

  • Vicky Choi
  • Pankaj K. Agarwal
  • Herbert Edelsbrunner
  • Johannes Rudolph
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)


We give an algorithm that locally improves the fit between two proteins modeled as space-filling diagrams. The algorithm defines the fit in purely geometric terms and improves by applying a rigid motion to one of the two proteins. Our implementation of the algorithm takes between three and ten seconds and converges with high likelihood to the correct docked configuration, provided it starts at a position away from the correct one by at most 18 degrees of rotation and at most 3.0Å of translation. The speed and convergence radius make this an attractive algorithm to use in combination with a coarse sampling of the six-dimensional space of rigid motions.


Rigid Motion Local Search Heuristic Docking Algorithm Bovine Pancreatic Trypsin Inhibitor Convergence Radius 
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 2004

Authors and Affiliations

  • Vicky Choi
    • 1
  • Pankaj K. Agarwal
    • 2
  • Herbert Edelsbrunner
    • 3
  • Johannes Rudolph
    • 4
  1. 1.Departments of Computer Science and BiochemistryDuke UniversityDurham
  2. 2.Departments of Computer Science and MathematicsDuke UniversityDurham
  3. 3.Departments of Computer Science and Mathematics, and Raindrop GeomagicDuke UniversityDurham
  4. 4.Departments of Biochemistry and ChemistryDuke UniversityDurham

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