Computational Biology of Protein Interactions

"How can macromolecular interactions be engineered in a rational manner to have the desired effects in a complex environment, such as a living organism?"

Answering this question is a major focus of much of the work carried out in the Green Lab. The interactions between biological macromolecules, and particularly proteins, play a fundamental role in biology, and while we have learnt a great deal about these interactions on many levels, our understanding is not yet at the level needed for the robust engineering of novel macromolecules. We are working on multiple fronts: to push forward the level of general understanding of biomolecular interections; to develop novel computational tools for the study and design of interacting macromolecules; and to directly apply our expertise to the rational design and engineering of proteins with real-world applicablity.

A major focus is on answering questions related to specificity:

  • What are the structural and energetic features that determine specific or promiscuous binding?
  • How does covalent modification, such as glycosylation, 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?
  • How can we achieve robust specificity in the interactions of rationally designed and engineered proteins?

  • Our choice of methods to solve these problems are primarily 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

  • Additionally, we currently are beginning an experimental component to our work, expressing, purifying and characterizing proteins which we have designed through rational computer-aided engineering.


    The Green Lab is an actived member of a number of interdisciplinary groups that bring together scientists from a range of Stony Brook departments, as well as individuals at Brookhaven National Laboratory. For students interested in graduate study, we are affiliated with several graduate programs which suit students from diverse backgrounds. We are additionally affiliated with summer research programs for undergraduates and high-school students who are interested in gaining hands-on experience in research.

    Programs for graduate study

  • Computational Biology Group in AMS
  • Graduate Program in Biochemistry & Structural Biology
  • Department of Chemistry
  • Summer research programs

  • BioMath@StonyBrook: Undergraduate research opporunities at the interface of Biology & Mathematics
  • Simons Research Fellowships for high school students
  • Interdisciplinary research groups

  • Laufer Center for Computational Biology & Genome Sciences
  • Institute of Chemical Biology & Drug Discovery
  • Stony Brook Biosystems Group
  • New York Center for Computational Science
  • Brookhaven Computational Science Center