Boston University Superfund Research Program

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Bioinformatics Core

Principal Core Leader, Stefano Monti (Boston University School of Medicine, Department of Medicine)
Co-Leader, Sandor Vajda (Boston University, Department of Biomedical Engineering)

Offering computational tools, expertise, and help to certain projects in modeling and analysis of microarray data. Several research projects in this proposal focus on environmental pollutants that bind to specific protein receptors and impact regulatory pathways, resulting in developmental and reproductive abnormalities. In agreement with the research tools that are applicable to most projects in the proposal, the Bioinformatics and Molecular Modeling Research Support Core will develop and offer computational tools, expertise, and help in two areas: modeling the interactions between xenobiotics and protein receptors, including nuclear receptors and cytochrome P450s, using methods of structural bioinformatics and computational biology; and the statistical analysis of microarray data and the reconstruction of regulatory pathways. The particular function of the core include (1) developing and providing computational methods to address specific needs for the modeling of 3D structures of nuclear receptors and P450s, and their interactions with xenobiotics; (2) Developing a database of the interactions between environmental chemicals and relevant protein receptors; (3) providing assistance in the analyses of microarray data and the reconstruction of regulatory pathways affected by xenobiotics binding, and (4) collaborating with the PIs on the individual projects.

Project Leader: Sandor Vajda, Structural Bioinformatics Lab

PRECISE: (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products.

NURISITE: NuRISITE (Nuclear Receptor Interaction Site) is a database for identifying the interaction sites in 3-D structures of nuclear receptors, and for providing detailed information on the interactions between nuclear receptors (NRs) and their partners. (currently undergoing revision)

External Advisory Committee Presentation: A PDF of the presentation Dr. Vajda gave to the BU SRP External Advisory Committee on March 20, 2007.