Bioinformatics Core

Core Leaders

protein bioinformatics

Stefano Monti, Core Leader
Boston University School of Medicine, Department of Medicine

Sandor Vajda, Co-Leader
Boston University, Department of Biomedical Engineering

Core Description

The Bioinformatics and Molecular Modeling Research Support Core (BMMC) offers computational tools, expertise, and services to BUSRP projects (Project 3, 4, and 5, and interactions), in three areas: (1) analysis of data obtained by high throughput genomic technologies (microarray experiments and RNA-sequencing]), including reconstruction and visualization of regulatory pathways, and integration with data from public repositories; (2) development and application of a high-throughput expression profiling platform and associated computational models for the screening of chemical perturbations in vitro, which will allow the Projects’ investigators to analyze the transcriptional response to xenobiotics of interest, as well as the role played in it by the protein receptors and regulators under study, in multiple cellular contexts (cell lines); and (3) modeling interactions between xenobiotics and protein receptors and cytochrome P450s, using structural bioinformatics and computational biology, including tools originally developed for structure-based drug design, and further modified by the BMMC.


Structural Bioinformatics Lab

FTMap ( FTMap is a computational mapping server that identifies binding hot spots of macromolecules, i.e., regions of the surface with major contributions to the ligand binding free energy. To use FTMap, users submit a protein, DNA, or RNA structure in PDB format. FTMap samples billions of positions of small organic molecules used as probes and scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots, in good agreement with experimental data.

FTSite ( The goal of FTSite is the identification of ligand binding sites based on the structure of ligand-free proteins. The method is based on the observation that the binding site of a macromolecule generally includes a strong “main” hot spot and some other hot spots that are close enough to be reached by a ligand binding at the main hot spot. The program uses the consensus sites (CSs) detected via the FTMap server to identify and rank binding sites.

FTFlex ( FTFlex performs repeated mapping calculations while exploring low energy conformers of side chains in the vicinity of user-selected hot spots29. The primary goals of this approach are opening pockets in protein-protein interfaces that are potentially capable of binding small molecular inhibitors, and to determine the druggability of such sites.

FTMap/param ( FTMap/param enables the user to define small molecules that are not included in the standard FTMap probe set, to use the mapping program to generate low energy clusters of these additional molecules, and to check the locations of these clusters relative to the hot spots based on the original probes.


BUSRP Publications

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