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$F^2$Dock: Fast Fourier Protein-Protein Docking

Authors:

Chandrajit L. Bajaj,

Rezaul Chowdhury,

Vinay SiddahanavalliAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 8, Issue 1

Pages 45 - 58

https://doi.org/10.1109/TCBB.2009.57

Published: 01 January 2011 Publication History

Abstract

The functions of proteins are often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination, and understanding function and structure relationships. In this paper, we extend our nonuniform fast Fourier transform-based docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code {\rm F}^2Dock (F^2= {\rm \underline{F}ast\underline{F}ourier}). We have calibrated {\rm F}^2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that {\rm F}^2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic-potential-based scores only, {\rm F}^2Dock is structured to incorporate Lennard-Jones potential and reranking docking solutions based on desolvation energy .

References

[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, R.A. 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.

Digital Library

[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.

Digital Library

[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.

Digital Library

[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.

Digital Library

[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]

M.L. Connolly, "Shape Complementarity at the Hemoglobin ¿₁ß₁ 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.

Digital Library

[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 ß-Lactamase Inhibitory Protein to Tem-1 ß-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, 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, 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, V.A. 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.

Digital Library

[37]

J.A. Kovacs and W. Wriggers, "Fast Rotational Matching," Acta Crystallographica, Biological Crystallography, vol. D58, no. 8, pp. 1282-1286, Aug. 2002.

[38]

J.A. Kovacs, P. Chacó n, 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 c ² 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.

Digital Library

Cited By

Sudha SBaskar SKrishnaswamy S(2022)Protein docking using constrained self-adaptive differential evolution algorithmSoft Computing - A Fusion of Foundations, Methodologies and Applications10.1007/s00500-018-03717-223:22(11651-11669)Online publication date: 11-Mar-2022
https://dl.acm.org/doi/10.1007/s00500-018-03717-2
Axenopoulos ADaras PPapadopoulos GHoustis E(2013)SP-DockIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2012.14910:1(135-150)Online publication date: 1-Jan-2013
https://dl.acm.org/doi/10.1109/TCBB.2012.149

$F^2$Dock: Fast Fourier Protein-Protein Docking
1. Applied computing
  1. Life and medical sciences

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cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 8, Issue 1

January 2011

282 pages

ISSN:1545-5963

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IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 January 2011

Published in TCBB Volume 8, Issue 1

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Cited By

Sudha SBaskar SKrishnaswamy S(2022)Protein docking using constrained self-adaptive differential evolution algorithmSoft Computing - A Fusion of Foundations, Methodologies and Applications10.1007/s00500-018-03717-223:22(11651-11669)Online publication date: 11-Mar-2022
https://dl.acm.org/doi/10.1007/s00500-018-03717-2
Axenopoulos ADaras PPapadopoulos GHoustis E(2013)SP-DockIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2012.14910:1(135-150)Online publication date: 1-Jan-2013
https://dl.acm.org/doi/10.1109/TCBB.2012.149

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