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Research Article

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

  • Yang Shen,

    Affiliations: BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America, Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America

    X
  • Ioannis Ch. Paschalidis,

    Affiliations: Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America, Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America

    X
  • Pirooz Vakili,

    Affiliations: Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America, Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America, Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America

    X
  • Sandor Vajda mail

    vajda@bu.edu

    Affiliation: BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America

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  • Published: October 10, 2008
  • DOI: 10.1371/journal.pcbi.1000191

About the Authors

Yang Shen, Sandor Vajda
BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili
Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America
Ioannis Ch. Paschalidis, Pirooz Vakili
Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America
Ioannis Ch. Paschalidis
Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
Pirooz Vakili
Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America

Corresponding Author

Email: vajda@bu.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: YS ICP PV SV. Performed the experiments: YS. Analyzed the data: YS. Wrote the paper: YS ICP PV SV.