Overview

Our laboratory is located on the fifth floor of the Biochemistry Building in Room 502C, is 1000 sq. ft. in area. It has been remodeled as a molecular graphics and computational laboratory with an enclosed graphics lab, computational office space, and a chilled computer room. There is comfortable desk space for ten researchers.

Computational Equipment

Computational resources include 12 Dell PC's running RedHat Enterprise Linux or CentOS for computing; including two Xeon 3.1 GHz, one Xeon 3.4 GHz, two Xeon 3.6 GHz, one Xeon 3.2 GHz, and one Xeon 3.0 GHz dual-processor systems with 2+GB RAM each; one Celeron 2.4 GHz processor, and one 2.8 GHz Pentium IV machine; and a dedicated laboratory firewall and switch. We have three Pentium IV 1.8-2.4 GHz PC's running Windows XP and one Windows laptop; plus two Silicon Graphics (SGI) R12000 300 MHz IRIX 6.5 workstations with SSE/MXE stereographics and 512MB RAM for interactive 3D graphics. The lab has over 4 TB of disk space with user files protected by daily/weekly incremental and monthly full back-ups onto USB external drives.

Peripheral Equipment

Peripherals include HP and Canon B&W and color laser/inkjet printers, two color scanners, color fax/copiers, and internal/external DVD/CD burners.

Software

Our software collection includes:

• OpenEye software including Omega, QuACPac, Vida, EON, ROCS, OEChem, and Szybki
• Accelrys's InsightII and Biopolymer packages
• Molecular mechanics packages CHARMM and MMTSB, AMBER, and GROMACS
• Molecular design/optimization programs BOMB and AlleGrow
• QikProp for filtering molecular databases according to drug-likeness and other physicochemical properties; Corina for building 3D structures from 2D specifications
• Crystallographic and structural analysis packages XtalView, Molecular Surface Package, WhatIf, PyMol, ProAct, ProCheck, and Reduce
• Docking tools DOCK (UCSF) and AutoDock (Scripps)
• Scoring tools DrugScore, DrugScore(CSD), and Xscore
• Origin and Matlab statistical and mathematical analysis software
• Regular updates of the Protein Data Bank (PDB), Cambridge Crystallographic Database (CSD) and its IsoStar interaction library, and the ZINC commercially available drug-like compound database (currently 2.1 million compounds)
• C, C++, Python, Ruby, and FORTRAN compilers and debuggers
• Publishing tools Adobe Illustrator, Photoshop, ChemDraw, TeX/LaTeX/BibTeX, GIMP, Reference Manager and EndNote
• Access to CAS Registry, SciFinder, Medline, and many other online reference collections