Links Related to DOCKing

Required for DOCKing

  • MPICH Library: library required to compile MPI function
  • Cygwin: Linux-like environment required to run Windows version of DOCK
  • g77 3.4: fortran compiler required to run accessory programs on Mac
  • dms: computes molecular surface of molecule

Other Useful Programs

  • babel: interconverts file formats used in molecular modeling
  • Sybyl: visualization and computation of chemical properties
  • Moe: visualization and computation of chemical properties
  • Quac Pac: pKa and tautomer enumeration in order to get correct protonation states and partial charge calculation (Open Eye)
  • Chimera: UCSF molecular modeling
  • Molecular Visualization Freeware: UMass, Amherst
  • Vida: Open Eye
  • PyMol: DeLano Scientific

Other Modeling Programs

  • AMBER: Molecular Dynamics simulation package
  • MORDOR: Fully flexible docking package

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