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Boston University

Superfund Research Program

Bioinformatics and Molecular Modeling

Project Leader: Sandor Vajda
Grant Number: P42ES007381
Funding Period: 2000-2020

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Project Summary (2000-2005)

Several research projects in this program focus on environmental pollutants that bind to specific protein receptors and impact regulatory pathways, resulting in developmental and reproductive abnormalities. The bioinformatics and molecular modeling research support core facilitates the use of modern computational tools to study these interactions at the molecular level. Software and expert help is offered in four different areas: (1) bioinformatics, (2) molecular modeling and visualization, (3) protein structure prediction by homology modeling, and (4) analysis of receptor-ligand interactions. The bioinformatics tools include screening databases for similar sequences, aligning sequences for evolutionary inferences, and constructing evolutionary trees. The core provides a variety of molecular modeling and visualization tools for the analysis of DNA and protein structures. In particular, software packages and modeling expertise is provided for elucidating the tertiary structure of proteins that exhibit a reasonable degree of homology (at least 30% sequence identity) to a protein with known 3-D structure, thereby providing potentially valuable structural information in several research projects. Protein structures, obtained either experimentally or by homology modeling, are used to construct putative models of complexes with ligands of interest. Docking algorithms are provided for small organic molecules, flexible peptides, and proteins. The analysis of predicted receptor-ligand interactions suggests further experiments, and may help to elucidate the mechanism of action of the ligands under study. The core has programs to search entire databases of organic molicules for ligands with high affinity for a given receptor.

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