Computational Biochemistry and Proteomics


Computational Biochemistry and Proteomics

This research group is involved in two major projects and uses MSI software resources for routine applications.

  • One project focuses on anti-cancer and antimicrobial drug design that target enzymes like the proteasome or integral membrane proteins like cell surface growth receptors and transporters. For example, inhibition of the proteasome leads to cancer cell apoptosis or programmed cell death. This project requires access to the molecular modeling and simulation resources to perform molecular docking (e.g., with AUTODOCK and DOCK) and QSAR studies (e.g., with Tripos Sybyl , GAUSSIAN, and the Cambridge Structural Database) to guide the synthesis of novel hybrid inhibitors with some similarity to known scaffolds. Similar methods will be applied to other anti-microbial compounds.
  • The second project is to identify the structure and function of a novel family of membrane-bound aspartyl proteases. This uses molecular modeling and simulation resources (e.g., Discovery Studio (Accelrys, Inc.) and PyMOL software packages) and will use structural biology resources (e.g., molecular dynamics software (Gromacs and NAMD) designed for biomolecular systems, biological force fields (CHARMm and AMBER), and docking software (AUTODOCK and DOCK)) in the future to perform docking studies in order to elucidate the preferred protein substrates for these proteases. In addition, this lab collaborates with the Center for Mass Spectrometry and their data are being stored on shared MSI/Mass Spec resources. They use a variety of the proteomics software packages (e.g., MAXQUANT, TINT, X! TANDEM, MASCOT, Scaffold Q+,and ProteinPilot ) for analyzing mass spectrometry data to identify proteins cleaved by their proteases.

In routine applications, the lab uses the Vector NTI software package for molecular biology and genetic engineering applications, the software for data analysis, curve fitting, and graphing (e.g., Origin Lab software and GraphPad Prism), and MATLAB and Mathematica for numerical computation.

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