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]

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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