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Protein Docking Rong Chen Boston University

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BU Bioinformatics The Lowest Binding Free Energy G water R L R L L R L R L R

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BU Bioinformatics Protein Docking Using FFT R L L R R L Rotate Fast Fourier Transform Complex Conjugate Discretize Fast Fourier Transform SurfaceInterior Correlation function

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BU Bioinformatics Rotational Sampling Evenly distributed Euler angles Sampling IntervalNumber of angles 20°1,800 15°3,600 12°9,000 10°14,400 8°27,000 6°54,000 4°180,000

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BU Bioinformatics Performance Evaluation Success Rate: given the number of predictions(N p ), success rate is the percentage of complexes in the benchmark for which at least one hit has been obtained. Hit Count: the average number of hits over all complexes at a particular N p.

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BU Bioinformatics Rotational Sampling Density

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BU Bioinformatics Rotational Sampling Density

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BU Bioinformatics Protein Docking Using FFT R L L R R L Rotate Fast Fourier Transform Complex Conjugate Discretize Fast Fourier Transform SurfaceInterior Correlation function

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BU Bioinformatics Protein Docking Using FFT SurfaceInteriorBinding Site Y Translation Correlation X Translation IFFT Increase the speed by 10 7

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BU Bioinformatics An Effective Binding Free Energy Function van der Waals energy; Shape complementarity Desolvation energy; Hydrophobicity Electrostatic interaction energy Translational, rotational and vibrational free energy changes Number of atom pairs of type i Desolvation energy for an atom pair of type i

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BU Bioinformatics 9i9i9i9i9i9i9i9i9i9i 9i9i9i9i9i9i9i9i9i9i 9i9i9i9i9i9i 9i9i9i9i9i9i 9i9i9i9i9i9i9i9i9i9i 9i9i9i9i9i9i9i9i9i9i 11 11111 11 111 111 11 11 11111 1 119i9i 119i9i9i9i1 11 1 9i9i 1 R GSC L GSC Grid-based Shape Complementarity

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BU Bioinformatics R PSC L PSC 1+3i 1+9i 1+3i 1+9i 1+3i 1+9i 1+3i 3i3i3i3i3i3i3i3i3i3i 3i3i9i9i3i3i3i3i3i3i 3i3i9i9i3i3i 3i3i9i9i3i3i 3i3i9i9i3i3i3i3i3i3i 3i3i3i3i3i3i3i3i3i3i 22 33232 23 523 523 23 22 33232 1 1 1 11 1 Pairwise Shape Complementarity

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BU Bioinformatics PSC vs. GSC on Success Rate

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BU Bioinformatics PSC vs. GSC on Hit Count

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BU Bioinformatics Why PSC works better than GSC?

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BU Bioinformatics A B C D Why PSC works better than GSC?

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BU Bioinformatics A Receptor-Ligand Complex

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BU Bioinformatics An Effective Binding Free Energy Function van der Waals energy; Shape complementarity Desolvation energy; Hydrophobicity Electrostatic interaction energy Translational, rotational and vibrational free energy changes Number of atom pairs of type i-j Desolvation energy for an atom pair of type i-j

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BU Bioinformatics Impact of Desolvation and Electrostatics

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BU Bioinformatics Impact of Desolvation and Electrostatics

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BU Bioinformatics Other available Docking Software Fast Fourier Transform or FFT (Katchalski- Katzir, Sternberg, Vakser, Ten Eyck groups) Computer vision based method (Nussinov group, 1999) Boolean operations (Palma et al., 2000) Polar Fourier correlations (Ritchie & Kemp, 2000) Genetic algorithm (Gardiner, Burnett groups) Flexible docking (Abagyan, 2002)

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BU Bioinformatics 3D-Dock Michael J.E. Sternberg, Imperial Cancer Research Fund, London, UK. FTDock: Grid-based shape complementarity, FFT. RPScore: empirical pair potential. MultiDock: refinement. http://www.bmm.icnet.uk/docking/index.html

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BU Bioinformatics GRAMM Ilya A. Vakser, State University of New York at Stony Brook. Geometric fit and hydrophobicity FFT Low resolution docking http://reco3.ams.sunysb.edu/gramm/

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BU Bioinformatics DOT Lynn F. Ten Eyck, University of California, San Diego. Grid-based shape complemetarity, elctrostatics FFT http://www.sdsc.edu/CCMS/Papers/DOT_sc95. html

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BU Bioinformatics ICM Ruben Abagyan, The Scripps Research Institute, La Jolla. Pseudo-Brownian rigid-body docking Biased Probability Monte Carlo Minimization of the ligand interacting side-chains. http://abagyan.scripps.edu/lab/web/man/f rames.htm

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BU Bioinformatics HEX Dave Ritchie, University of Aberdeen, Aberdeen, Scotland, UK spherical polar Fourier correlations http://www.biochem.abdn.ac.uk/hex/

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BU Bioinformatics Approach Overview PDB1 PDB2 PDB Processing ZDOCK: Initial-stage Docking RDOCK: Refinement-stage Docking Clustering Final 10 predictions Biological information

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BU Bioinformatics Example: CAPRI Target 6: α-amylase / Camelid VHH domain

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