Advertisement

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)

Abstract

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.

Keywords

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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Agarwal, P.K., Edelsbrunner, H., Harer, J., Wang, Y.: Extreme elevation on a 2-manifold. In: Proc. 20th Ann. Sympos. Comput. Geom., pp. 357–365 (2004)Google Scholar
  2. 2.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acid Res 28, 235–242 (2000)CrossRefGoogle Scholar
  3. 3.
    Bespamyatnikh, S., Choi, V., Edelsbrunner, H., Rudolph, J.: Accurate bound protein docking by shape complementarity. Manuscript, Dept. Comput. Sci., Duke Univ., Durham, North Carolina (2003)Google Scholar
  4. 4.
    Brooks, B.R., Karplus, M.: Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. 80, 3696–3700 (1983)CrossRefGoogle Scholar
  5. 5.
    Camacho, C.J., Vajda, S.: Protein docking along smooth association pathways. Proc. Natl. Acad. Sci. 98, 10636–10641 (2001)CrossRefGoogle Scholar
  6. 6.
    Choi, V., Goyal, N.: A combinatorial shape matching algorithm for rigid protein docking. In: Proc. 15th Ann. Sympos. Combin. Pattern Matching (2004) (to appear)Google Scholar
  7. 7.
    Elcock, A.H., Sept, D., Mccammon, J.A.: Computer simulation of protein-protein interactions. J. Phys. Chem. 105, 1504–1518 (2001)Google Scholar
  8. 8.
    Fernandez-Recio, J., Totrov, M., Abagyan, R.: Soft protein-protein docking in internal coordinates. Protein Sci. 11, 280–291 (2002)CrossRefGoogle Scholar
  9. 9.
    Halperin, D., Overmars, M.H.: Spheres, molecules, and hidden surface removal. Comput. Geom. Theory Appl. 11, 83–102 (1998)zbMATHMathSciNetGoogle Scholar
  10. 10.
    Halperin, B., Ma, H., Wolfson, R.: Nussinov. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 47, 409–443 (2002)CrossRefGoogle Scholar
  11. 11.
    Horn, B.K.P.: Closed-form solution of absolute orientation using unit quaternions. J. Opt. Soc. Amer. A 4, 629–642 (1987)CrossRefGoogle Scholar
  12. 12.
    Jacobs, D.J., Rader, A.J., Kuhn, L.A., Thorpe, M.F.: Protein flexibility predictions using graph theory. Proteins 44, 150–165 (2001)CrossRefGoogle Scholar
  13. 13.
    Janin, J., Wodak, S.J.: The structural basis of macromolecular recognition. Adv. Protein Chem. 61, 9–73 (2002)CrossRefGoogle Scholar
  14. 14.
    Jiang, F., Kim, S.-H.: Soft-docking”: matching of molecular surface cubes. J. Mol. Biol. 219, 79–102 (1991)CrossRefGoogle Scholar
  15. 15.
    Kabsch, W.: A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. Sect. A 34, 827–828 (1978)CrossRefGoogle Scholar
  16. 16.
    Lorber, D.M., Udo, M.K., Shoichet, B.K.: Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci. 11, 1393–1408 (2002)CrossRefGoogle Scholar

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

Personalised recommendations