Computational Biology of Protein Interactions

The interactions between proteins play a fundamental role in biology, and while we have learnt a great deal about these interactions on many levels, many questions remain. Among these are basic questions of specificity:

  • What are the structural and energetic features that determine specific or promiscuous binding?

  • How does covalent modification affect the interaction profile of a given protein?

  • What are the consequences of varying specificity of interaction on the systems-level behavior of a biochemical network?

    • Our lab is working to answer some of these problems using the tools of computational biology. We employ a range of models and computational methods, including:

  • Continuum electrostatic analysis of binding energetics

  • Molecular dynamics simulations

  • Discrete conformational search and methods for protein design

  • Bayesian (probablistic) modeling of signaling pathways

  • Dynamic models of biochemical networks

    • Affiliations

    Computational Biology Group in AMS

    Graduate Program in Biochemistry & Structural Biology

    Institute of Chemical Biology & Drug Discovery

    Stony Brook Biosystems Group

    Brookhaven Computational Science Center