SciPy2004 FlexTree Package Yong Zhao The Molecular Graphics Laboratory The Scripps Research Institute,La Jolla,CA for computational biology.

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Presentation transcript:

SciPy2004 FlexTree Package Yong Zhao The Molecular Graphics Laboratory The Scripps Research Institute,La Jolla,CA for computational biology

SciPy2004 Overview  Background  FlexTree package  Development  Application of FlexTree  Summary

SciPy2004 Docking Study  ‘Lock and Key’ model  Induced Fit –50% of dockings fail because of induced-fit

SciPy2004 Background  Biological Molecules –Large conformational space  Docking Study –docking related conformational sub-space is relatively small –still too large to explore explicitly

SciPy2004 Example

SciPy2004 FlexTree Basic Objects Tree Node Shape Motion Shape-Motion Convolution Shape Combiner

SciPy2004

<root file="1hvrLigRotated.pdbqs" name="1hvr" id="99" selectionString="1hvrLigRotated" convolve="FTConvolveApplyMatrix"> <node name="chainA" id="1" selectionString="1hvrLigRotated:A" convolve="FTConvolveApplyMatrixToCoords"> <node name="CoreA" id="2" selectionString="1hvrLigRotated:A:,PRO1-GLU34,…“ motion="FTMotion_Generic“ motionParams="matrixList:list float …“ shape="FTLines“ shapeParams="cutoff:float1.85" convolve="FTConvolveApplyMatrixToCoords"> <node... XML

SciPy2004 Programming  Python –PMV (Python Molecule Viewer) –Vision (Previously know as ViPEr ) –SciPy (Genetic Algorithm package)  C++ –Scoring function –Computational intensive

SciPy2004 Application of FlexTree Searching the conformational sub-space

SciPy2004 FlexTree-based Computations Automated Docking

SciPy2004 Genetic Algorithm Hinge Float: hinge angle Genome The motion parameters are used as ‘Genes’

SciPy2004 Docking Test Result  Population size = 500, converges after 91 generations  the best docked conformation –interaction energy : Kcal/mol –compare with experimental result : Kcal/mol –RMSD = 0.35 Å (all atoms ) v.s. crystal structure

SciPy2004 FlexTree Summary  Represents the flexibility hierarchically ✔ Given knowledge of protein flexibility ✔ Conformational sub-space ✔ Tree structure  Real-time 3D Visualization  Python & C++  Conformation search & Docking test 

SciPy2004 Acknowledgment - Dr.Michel Sanner - Dr.Daniel Stoffler - The Molecular Graphics TSRI - SciPy community - NBCR National Biomedical Computational Resources - NIH Grant BISTI,R21/R33GM65609