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Protein Structural Analysis Laboratory Facilities

Michigan State University
502C Biochemistry Building
E. Lansing, MI 48824-1319

Ph: (517) 353-8745  Fax: (517) 353-9334

Model for how monoclonal antibody 3D6 (yellow and green tubes) can recognize a helical peptide (blue) in Brugia malayi asparaginyl-tRNA synthetase and neutralize its enzymatic activity by occluding the active site.  See M. A. Kron et al. (2008), under Publications.
Protein Structural Analysis Laboratory

Laboratory Facilities

Overview

Urease trimer of trimers consisting of the A (red), B (blue), and C (green) subunits.  The B subunit shifts to allow C subunit active site access during enzyme activation, via a conformational transition of its tether region (white).  (See Quiroz-Valenzuela et al., 2008, under Publications.)

Our laboratory is located on the fifth floor of the Biochemistry Building in Room 502C, with 1000 square feet of molecular graphics and computational laboratory space, including an enclosed graphics lab and chilled computer room.

Computational Equipment

Computational resources include 36 Dell Xeon processors (2.1-3.6GHz; 3-16GB RAM) running RedHat Enterprise or CentOS Linux for molecular computation and graphics. PBS is used for job management across our multiprocessor cluster. We have more than 15 Terabytes of disk space, with daily data backups onto external drives and a dedicated laboratory firewall and switch. Peripherals include B&W and color laser printers and scanners/copiers.

Software

Our software collection includes:

  • OpenEye Omega, QUACPAC, Vida, EON, ROCS, and OEChem
  • Molecular mechanics packages YASARA Structure, CHARMM and MMTSB, AMBER, GROMACS, and ProFlex
  • Crystallographic, modeling, and structural analysis packages Chimera, MODELLER, ProAct, ProCheck, PyMOL, Reduce, and WhatIf
  • Docking tools SLIDE, AutoDock, AutoDock Vina, and GOLD
  • Molecular interaction scoring by SLIDE_score, DrugScore(PDB), DrugScore(CSD), DrugScoreX, and LigScore
  • MATLAB and R statistical and mathematical analysis software
  • Regular updates of the Protein Data Bank, Cambridge Structural Database, and CAS Registry/SciFinder
  • C, C++, Python, and FORTRAN compilers and debuggers