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Protein–Protein Docking: Overview and Performance Analysis

  • Kevin Wiehe
  • Matthew W. Peterson
  • Brian Pierce
  • Julian Mintseris
  • Zhiping Weng
Part of the Methods in Molecular Biology™ book series (MIMB, volume 413)

Summary

Protein–protein docking is the computational prediction of protein complex structure given the individually solved component protein structures. It is an important means for understanding the physicochemical forces that underlie macromolecular interactions and a valuable tool for modeling protein complex structures. Here, we report an overview of protein–protein docking with specific emphasis on our Fast Fourier Transform-based rigid-body docking program ZDOCK, which is consistently rated as one of the most accurate docking programs in the Critical Assessment of Predicted Interactions (CAPRI), a series of community-wide blind tests. We also investigate ZDOCK’s performance on a non-redundant protein complex benchmark. Finally, we perform regression analysis to better understand the strengths and weaknesses of ZDOCK and to suggest areas of future development for protein-docking algorithms in general.

Keywords

Protein–protein docking ZDOCK RDOCK Fast Fourier Transform benchmark CAPRI shape complementarity electrostatics desolvation energy regression analysis 

Notes

Acknowledgments

We are grateful to the Scientific Computing Facilities at Boston University and the Advanced Biomedical Computing Center at NCI, NIH for support in computing. This work was funded by NSF grants DBI-0133834 and DBI-0116574.

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Copyright information

© Humana Press Inc 2008

Authors and Affiliations

  • Kevin Wiehe
  • Matthew W. Peterson
  • Brian Pierce
  • Julian Mintseris
  • Zhiping Weng

There are no affiliations available

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