F2dock: Fast fourier protein-protein docking

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 8, Issue 1, 2011, Pages 45-58

  Bajaj, Chandrajit L ^a   Chowdhury, Rezaul ^a   Siddahanavalli, Vinay ^b  

^a University of Texas at Austin ^*  (United States)

^b GOOGLE INC   (United States)

Author keywords

algorithms; Computational structural biology; docking; fast Fourier transform; protein protein interactions; redocking.

Indexed keywords

ADAPTIVE SEARCH; DESOLVATION ENERGY; DOCKING ALGORITHMS; DOCKING SOLUTIONS; DRUG DESIGN; EXPERIMENTAL STUDIES; FOURIER; LENNARD-JONES POTENTIAL; MULTI-CORE MACHINES; MULTITHREADED; MUTUAL INTERACTION; NON-UNIFORM FAST FOURIER TRANSFORMS; PROTEIN-PROTEIN DOCKING; PROTEIN-PROTEIN INTERACTIONS; RE-RANKING; REDOCKING.; RELATIVE TRANSFORMATION; SHAPE COMPLEMENTARITY; SPEED-UPS; STABLE COMPLEXES; STRUCTURAL BIOLOGY; STRUCTURE DETERMINATION;

ADAPTIVE ALGORITHMS; COMPLEXATION; DOCKING; DOCKS; FAST FOURIER TRANSFORMS; HYDRAULIC STRUCTURES;

PROTEINS;

RUMEX;

BACTERIAL PROTEIN; PROTEIN;

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; BIOLOGY; CATTLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; FOURIER ANALYSIS; HUMAN; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN BINDING; STATIC ELECTRICITY; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; BINDING SITES; CATTLE; COMPUTATIONAL BIOLOGY; FOURIER ANALYSIS; HUMANS; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE; STATIC ELECTRICITY;

EID: 78449292668     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2009.57     Document Type: Article

References (55)

1. J. S. Fruton, Proteins, Enzymes, Genes: The Interplay of Chemistry and Biology. Yale Univ. Press, 1999.
2. A. R. Leach, Molecular Modelling: Principles and Applications, second ed., Pearson Education EMA, 2001.
3. H. A. Gabb, R. M. Jackson, and M. J. E. Sternberg, "Modelling Protein Docking Using Shape Complementarity, Electrostatics and Biochemical Information, " J. Molecular Biology, vol. 272, no. 1, pp. 106-120, Sept. 1997.
4. I. M. Klotz, Ligand-Receptor Energetics: A Guide for the Perplexed. John Wiley and Sons, 1997.
5. J. Castrillon-Candas, V. Siddavanahalli, and C. Bajaj, "Nonequispaced Fourier Transforms for Protein-Protein Docking, " ICES Report 05-44, Univ. of Texas at Austin, Oct. 2005.
6. J. Mintseris, K. Wiehe, B. Pierce, R. Anderson, R. Chen, J. Janin, and Z. Weng, "Protein-Protein Docking Benchmark 2.0: An Update, " Proteins: Structure, Function, and Bioinformatics, vol. 60, no. 2, pp. 214-216, http://zlab.bu.edu/zdock/benchmark.shtml, 2005.
7. C. Bajaj, RA. Chowdhury, and V. Siddavanahalli, "F3Dock: A Fast, Flexible and Fourier Based Approach to Protein-Protein Docking, " ICES Report 08-01, Univ. of Texas at Austin, Jan. 2008.
8. T. Ewing, "Automated Molecular Docking: Development and Evaluation of New Search Methods, " PhD thesis, Univ. of California, 1997.
9. M. D. Miller, S. K. Kearsley, D. J. Underwood, and R. P. Sheridan, "FLOG: A System to Select Quasi-Flexible Ligands Complementary to a Receptor of Known Three-Dimensional Structure, " J. Computer-Aided Molecular Design, vol. 8, no. 2, pp. 153-174, 1994.
10. B. K. Shoichet, D. L. Bodian, and I. D. Kuntz, "Molecular Docking Using Shape Descriptors, " J. Computational Chemistry, vol. 13, no. 3, pp. 380-397, 1992.
11. I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge, and T. E. Ferrin, "A Geometric Approach to Macromolecule-Ligand Interactions, " J. Molecular Biology, vol. 161, no. 2, pp. 269-288, Oct. 1982.
12. B. K. Shoichet and I. D. Kuntz, "Protein Docking and Complementarity, " J. Molecular Biology, vol. 221, no. 1, pp. 327-346, Sept. 1991.
13. D. Fischer, R. Norel, R. Nussinov, and H. J. Wolfson, "3-D Docking of Protein Molecules, " Proc. Fourth Ann. Symp. Combinatorial Pattern Matching (CPM'93), pp. 20-34, 1993.
14. R. Norel, D. Fischer, H. J. Wolfson, and R. Nussinov, "Molecular Surface Recognition by a Computer Vision-Based Technique, " Protein Eng., vol. 7, no. 1, pp. 39-46, Jan. 1994.
15. R. Norel, S. L. Lin, H. J. Wolfson, and R. Nussinov, "Molecular Surface Complementarity at Protein-Protein Interfaces: The Critical Role Played by Surface Normals at Well Placed, Sparse, Points in Docking, " J. Molecular Biology, vol. 252, no. 2, pp. 263-273, Sept. 1995.
16. D. Fischer, S. L. Lin, H. L. Wolfson, and R. Nussinov, "A Geometry-Based Suite of Molecular Docking Processes, " J. Molecular Biology, vol. 248, no. 2, pp. 459-477, 1995.
17. D. Duhovny, R. Nussinov, and H. J. Wolfson, "Efficient Unbound Docking of Rigid Molecules, " Proc. Fourth Int'l Workshop Algorithms in Bioinformatics, R. Guigo and D. Gusfield, eds., pp. 185-200, Sept. 2002.
18. H.-P. Lenhof, "New Contact Measures for the Protein Docking Problem, " Proc. First Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB'97), pp. 182-191, 1997.
19. F. S. Kuhl, G. M. Crippen, and D. K. Friesen, "A Combinatorial Algorithm for Calculating Ligand Binding, " J. Computational Chemistry, vol. 5, no. 1, pp. 24-34, 1984.
20. 1 Subunit Interface, " Biopolymers, vol. 25, no. 7, pp. 1229-1247, Feb. 1986.
21. H. Wang, "Grid-Search Molecular Accessible Surface Algorithm for Solving the Protein Docking Problem, " J. Computational Chemistry, vol. 12, no. 6, pp. 746-750, 1991.
22. F. Jianga and S.-H. Kim, "'Soft Docking': Matching of Molecular Surface Cubes, " J. Molecular Biology, vol. 219, no. 1, pp. 79-102, May 1991.
23. N. C. J. Strynadka, M. Eisenstein, E. Katchalski-Katzir, B. K. Shoichet, I. D. Kuntz, R. Abagyan, M. Totrov, J. Janin, J. Cherfils, F. Zimmerman, A. Olson, B. Duncan, M. M. Rao, R. Jackson, M. Sternberg, and M. N. G James, "Molecular Docking Programs Successfully Predict the Binding of a β-Lactamase Inhibitory Protein to Tem-1 β-Lactamase, " Nature Structural Biology, vol. 3, pp. 233-239, 1996.
24. S. Belongie, J. Malik, and J. Puzicha, "Matching Shapes, " Proc. IEEE Int'l Conf. Computer Vision, vol. 1, pp. 454-461, 2001.
25. E. Katchalski-Katzir, I. Shariv, M. Eisenstein, AA. Friesem, C. Aflalo, and I. A. Vakser, "Molecular Surface Recognition: Determination of Geometric Fit between Proteins and Their Ligands by Correlation Techniques, " Proc. Natl Academy of Sciences USA, vol. 89, no. 6, pp. 2195-2199, 1992.
26. D. W. Ritchie and G. J. Kemp, "Protein Docking Using Spherical Polar Fourier Correlations, " Proteins: Structure, Function, and Genetics, vol. 39, no. 2, pp. 178-194, Mar. 2000.
27. J. G Mandell, VA. Roberts, M. E. Pique, V. Kotlovyi, J. C. Mitchell, E. Nelson, I. Tsigelny, and L. F. T. Eyck, "Protein Docking Using Continuum Electrostatics and Geometric Fit, " Protein Eng., vol. 14, no. 2, pp. 105-113, Feb. 2001.
28. R. Chen and Z. Weng, "Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics, " Proteins: Structure, Function, and Genetics, vol. 47, no. 3, pp. 281-294, Mar. 2002.
29. R. Chen, L. Li, and Z. Weng, "ZDOCK: An Initial-Stage Protein-Docking Algorithm, " Proteins: Structure, Function, and Genetics, Special Issue: CAPRI-Critical Assessment of PRedicted Interactions, Issue Edited by Joël Janin, vol. 52, no. 1, pp. 80-87, May 2003.
30. R. Chen and Z. Weng, "A Novel Shape Complementarity Scoring Function for Protein-Protein Docking, " Proteins: Structure, Function, and Genetics, vol. 51, no. 3, pp. 397-408, Mar. 2003.
31. L. Li, R. Chen, and Z. Weng, "RDOCK: Refinement of Rigid-Body Protein Docking Predictions, " Proteins: Structure, Function, and Genetics, vol. 53, no. 3, pp. 693-707, Sept. 2003.
32. M. Meyer, P. Wilson, and D. Schomburg, "Hydrogen Bonding and Molecular Surface Shape Complementarity as a Basis for Protein Docking, " J. Molecular Biology, vol. 264, no. 1, pp. 199-210, Nov. 1996.
33. D. W. Ritchie, "Parametric Protein Shape Recognition, " PhD thesis, Depts. of Computer Science & Molecular and Cell Biology, Univ. of Aberdeen, King's College, Aberdeen, UK, Sept. 1998.
34. D. W. Ritchie and G. J. L. Kemp, "Fast Computation, Rotation, and Comparison of Low Resolution Spherical Harmonic Molecular Surfaces, " J. Computational Chemistry, vol. 20, no. 4, pp. 383-395, Feb. 1999.
35. B. S. Duncan and A. J. Olson, "Approximation and Characterization of Molecular Surfaces, " Biopolymers, vol. 33, pp. 219-229, 1993.
36. N. L. Max and E. D. Getzoff, "Spherical Harmonic Molecular Surfaces, " IEEE Computer Graphics and Applications, vol. 8, no. 4, pp. 42-50, July 1988.
37. JA. Kovacs and W. Wriggers, "Fast Rotational Matching, " Acta Crystallographica, Biological Crystallography, vol. D58, no. 8, pp. 1282-1286, Aug. 2002.
38. JA. Kovacs, P. Chacón, Y. Cong, E. Metwally, and W. Wriggers, "Fast Rotational Matching of Rigid Bodies by Fast Fourier Transform Acceleration of Five Degrees of Freedom, " Acta Crystallographica, Biological Crystallography, vol. D59, no. 8, pp. 1371-1376, Aug. 2003.
39. D. J. Bacon and J. Moult, "Docking by Least-Squares Fitting of Molecular Surface Patterns, " J. Molecular Biology, vol. 225, no. 3, pp. 849-858, June 1992.
40. P. H. Walls and M. J. E. Sternberg, "New Algorithm to Model Protein-Protein Recognition Based on Surface Complementarity. Applications to Antibody-Antigen Docking, " J. Molecular Biology, vol. 228, no. 1, pp. 277-297, Nov. 1992.
41. M. Helmer-Citterich and A. Tramontano, "PUZZLE: A New Method for Automated Protein Docking Based on Surface Shape Complementarity, " J. Molecular Biology, vol. 235, no. 3, pp. 1021-1031, Jan. 1994.
42. A. Fahmy and G. Wagner, "TreeDock: A Tool for Protein Docking Based on Minimizing van der Waals Energies, " J. Am. Chemical Soc., vol. 124, no. 7, pp. 1241-1250, Feb. 2002.
43. S.-Y. Yue, "Distance-Constrained Molecular Docking by Simulated Annealing, " Protein Eng., vol. 4, no. 2, pp. 177-184, Dec. 1990.
44. J. Cherfils, S. Duquerroy, and J. Janin, "Protein-Protein Recognition Analyzed by Docking Simulation, " Proteins: Structure, Function, and Genetics, vol. 11, no. 4, pp. 271-280, 1991.
45. R. Gabdoulline and R. Wade, "Analytically Defined Surfaces to Analyze Molecular Interaction Properties, " J. Molecular Graphics, vol. 14, no. 6, pp. 341-353, Dec. 1996.
46. C. Bajaj, G. Xu, and Q. Zhang, "A Fast Variational Method for the Construction of Resolution Adaptive c2 Smooth Molecular Surfaces, " Computer Methods in Applied Mechanics and Eng., vol. 198, pp. 1684-1690, 2009.
47. E. Katchalski-Katzir, I. Shariv, M. Eisenstein, A. A. Friesem, C. Aflalo, and I. A. Vakser, "Molecular Surface Recognition: Determination of Geometric Fit between Proteins and Their Ligands by Correlation Techniques, " Proc. Nat'l Academy of Sciences USA, vol. 89, no. 6, pp. 2195-2199, Mar. 1992.
48. "PDB2PQR: An Automated Pipeline for the Setup, Execution, and Analysis of Poisson-Boltzmann Electrostatics Calculations, " http://pdb2pqr.sourceforge.net/, 2010.
49. D. Potts, G. Steidl, and M. Tasche, "Fast Fourier Transform for Nonequispaced Data: A Tutorial, " Modern Sampling Theory: Mathematics and Applications, ch. 12, pp. 247-270, Birkhäuser, 2001.
50. W. Kabsch, "A Solution for the Best Rotation to Relate Two Sets of Vectors, " Acta Crystallographica Section A, vol. 32, pp. 922-923, 1976.
51. W. Kabsch, "A Discussion of the Solution for the Best Rotation to Relate Two Sets of Vectors, " Acta Crystallographica Section A, vol. 34, no. 5, pp. 827-828, Sept. 1978.
52. C. Bajaj and S.-C. Chen, "Efficient and Accurate Higher-Order Fast Multipole Boundary Element Method for Poisson Boltzmann Electrostatics, " TR 09-26, Dept. of Computer Sciences, Univ. of Texas at Austin, Apr. 2009.
53. M. Frigo and S. G. Johnson, "The Design and Implementation of FFTW3, " Proc. IEEE, Invited Paper, Special Issue on Program Generation, Optimization, and Platform Adaptation, vol. 93, no. 2, pp. 216-231, Feb. 2005.
54. The Message Passing Interface (MPI) Standard, http://www-unix. mcs.anl.gov/mpi/, 2010.
55. C. Bajaj, P. Djeu, V. Siddavanahalli, and A. Thane, "TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes, " Proc. Ann. IEEE Visualization Conf., pp. 243-250, 2004.