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Molecular Modeling

Molecular modeling resources

The interrelationship between NMR, X-ray crystallography, and molecular modeling ensures that molecular modeling will remain a cornerstone of the Structural Biology Shared Resource. Molecular graphics, computer-assisted drug design, QSAR, and related techniques can also be used to formulate working hypotheses that deal specifically with protein chemistry and drug development.

The data and hypotheses obtained through modeling studies can be examined or tested via chemical synthesis and/or biological evaluation of novel agents. The process is iterative: once preliminary pharmacological and cellular biological data are obtained, additional modeling studies can be employed to refine or re-define the working hypotheses.

The molecular modeling component of this shared resource provides and maintains the hardware and software suite necessary to support molecular modeling.

Currently supported hardware & software:


  • 6 Apple MacPro 8-core graphics workstations
  • 4 HP Linux 4-core graphics workstations
  • 2 Silicon Graphics Linux 4-core workstations
  • 2 Silicon Graphics Altix workstations
  • 1 Xerox/Tektronix Phaser 7750 color laser printer 

Shared Network Resources

  • 10TB RAID6 Disk storage system

Software and databases:

  • TRIPOS Sybyl suite
  • CCP4
  • Unity
  • DOCK
  • AutoDock
  • NAMD
  • GRID
  • Hex
  • HINT
  • Molconn-Z
  • GOLD
  • FlexX

The shared resource maintains a close working relationship with the VCU Center for High Performance Computing (CHiPC), which provides supercomputer-level hardware and software support for molecular simulation.