The ISB3D contains a University Core Facility in Molecular Modeling directed by Dr. Kellogg, assisted by Drs. J. Neel Scarsdale and Philip Mosier. It is part of VCU's Structural Biology Core. The Molecular Modeling facility offers modeling software and hardware resources to VCU researchers. The facility maintains an extensive library of commercial and academic modeling software with multi-user licenses for a number of key programs such as the Tripos suite (Sybyl, Unity, Surflex Dock, etc.). Other NMR, crystallography, and modeling software, e.g., CCP4, DOCK, HINT, Molconn-Z, ZAP, SCWRL, GRID, AutoDock, etc., are available on the ISBDD servers. At present, the modeling facility has 18 workstations (Apple MacPro and Linux), a local GPU cluster, and over 30 TB of disk storage controlled by a Linux server with a tape robot backup system. Many of the workstations are networked through gigabit ethernet to facilitate internal data transfers. The modeling facility offers two academic courses as a part of the Department of Medicinal Chemistry (MEDC 541 and MEDC 670) graduate program. A large number of VCU graduate students have received training in molecular modeling through this offering. Students enrolling in these courses come from over a dozen VCU departments on both the Monroe Park and Medical Center campuses.
modeling lab example [View Image]
The biophysical facility at the ISB3D consists of multiple instruments that support fundamental and applied research on mechanism of action, structure/activity relationships, and drug discovery and development. These instruments include a PTI spectrofluorometer, NanoTemper Microscale Thermophoresis, Reichert Surface Plasmon Resonance, Waters UPLC coupled to TQD-ESI-MS, Beckman Ultracentrifuge, Olis Circular Dichroism with stopped flow assembly, and dynamic light scattering.
The crystallography facility consists of Rigaku MicroMax-007HF X-ray Generator with VariMax-HF Arc Optics/Hybrid Photon Counter, Eiger R 4M Detector and AFC11 Goniometer, a desktop computer, a Haskris water chiller and a large collection of crystallographic software programs. The facility is used to collect X-ray diffraction data from small or macromolecule crystals and the data is subsequently used for structure elucidation. This instrument has been used by investigators from the Departments of Chemistry, Biochemistry, Physiology and Biophysics, Medicinal Chemistry and other units to deduce the structure of proteins and their complexes with drug like molecules. See the Facility Description for more.
Instruments for X-ray CRYSTALLOGRAPHY [View Image]
The Institute has incubator shakers for growing bacteria or yeast in up to 12 l scale at any temperature from 4 C-37 C or above. In addition the Institute houses a 35 l sterilizable in place New Brunswick 510 capable of growing bacteria or yeast under conditions of controlled temperature, pH, dissolved oxygen and volume, and the ability to collect the culture through a Beckman flow centrifuge in less than 2 hours.
The Institute for Structural Biology, Drug Discovery, and Development (ISB3D) has developed a high throughput screening (HTS) facility that is now open to researchers from within and outside VCU. Instrumentation that is currently available includes a BMG Labtech Clariostar microplate reader; BioTek MultiFlo FX plate washer and liquid dispenser; Combidrop nL liquid dispenser; and Labcyte Echo 550 acoustic liquid handler
(96-wells → 1534-wells).
The ISB3D hosts several libraries of chemical compounds with diverse structures including ApexBio* (FDA approved molecules; 2,000 compounds), Myria ScreenII** Diversity compound library from Sigma Aldrich (10,000 compounds, mol. wt. 120-500 Da). These 12,000 chemical compounds are available for HTS and biophysical analysis.
Myria Screen 2 [View Image]
ISB3D offers the following instruments to the VCU research community by reservation only:
Reservations are made thru the university's RAMS FORCE. Select the small reservations tab on the left side of page.
You are expected to be knowledgeable and trained in the use of the instruments.
First-time users of the X-Ray Diffractometer require completion of the "Radiation Safety Training For Research Employees" that can be found on Blackboard.
For access to the facility contact the appropriate faculty member.
Clariostar or Echo 550 contact Dr. Srinivas Sistla, firstname.lastname@example.org
X-Ray Diffractometer contact Dr. Faik Musayev, email@example.com