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FRED

Based on an original scientific perspective and efficient computational algorithms, FRED is an accurate and extremely fast docking program. With equivalent resolution settings, FRED will out-perform all known docking programs, typically examining about a dozen ligand conformers in a second. For each, FRED exhaustively examines all possible poses within the protein active site, filtering for shape complementarity and pharmacophoric features before scoring with more traditional functions.

When using a well-chosen set of conformers FRED predicts binding modes quite well.[1] Scientists at Roche concluded that “FRED as a docking engine is a good general method for structure-based virtual screening. Considering its high speed, FRED is certainly an especially attractive tool.”[2]

A pose predicted by FRED.

The crystallographic structure of a CDK-2 ligand in its bound conformation (green) overlaid by the pose predicted by FRED. Select image to enlarge.

The primary features of FRED include:

  • Systematic, nonstochastic, docking - reproducible results
  • ChemScore, PBSA, ChemGauss, PLP, ScreenScore
  • Customizable scoring functions and flexible consensus scoring methods
  • Multiple simultaneous scoring functions and hit lists
  • Refinement of docked poses in the context of the active site using MMFF, ala SZYBKI
  • Multiple Active Site Comparisons for promiscuity [3]
  • Directed docking with SMARTS enclosures
  • Docking analysis tools
  • OEChemplete - all I/O and molecular information processing by OEChem
  • Robust reading and specification-compliant writing of SDF, MOL, MOL2, PDB, MacroModel, XYZ, and OEBinary file formats
  • Support for LINUX, IRIX, Windows, OS X, AIX, HP-UX, Solaris, Tru64UNIX
  • 64-bit processing on IRIX, Itanium®2 Linux, PowerPC Linux, HP-UX and Tru64UNIX
  • Distributed processing via PVM for most Unix platforms

References

[1] Gaussian Docking Functions: McGann, M., Almond, H., Nicholls, A., Grant, J.A., and Brown, F., Biopolymers 2003, 68:76-90.

[2] Binding site characteristics in structure-based virtual screening, evaluation of current docking tools: Schulz-Gasch, T., and Stahl, M., J. Mol. Model. 2003, 9:47-57.

[3] Multiple Active Site Corrections for Docking and Virtual-Screening: Vigers, G.P., and Rizzi, J.P., J. Med. Chem. 47 (2004) 80-9.

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