Protein Substate Modeling and Identification Using the SVD


Tod D. Romo


Department of Biochemistry and Cell Biology
W. M. Keck Center for Computational Biology
Rice University

• Introduction
• The F46V Mutant Myoglobin
  • The Mutant
  • The F46V Crystallographic Structure
  • Time Averaged Refinement of F46V
• The Singular Value Decomposition
  • A Not So Small Problem with Time Averaged Refinements
  • Constructing the Singular Value Decomposition
  • SVD on the F46V Time Averaged Refinement
• The MbCO Myoglobin
  • The MbCO Dataset & Refinements
  • The Hand-Crafted Refinement
  • The Multi-Conformer Refinement
  • The Time Averaged Refinement
    • SVD Analysis of the Time Averaged Refinement
    • Comparison between the Time Averaged and Hand-Crafted Refinements
  • Comparing the different refinements
• Conclusions
• Acknowledgements