Ligand Docking and Scoring in Protein Receptor

FRED exhaustively examines all possible poses within the protein active site, filtering for shape complementarity [1] and pharmacophoric features before selecting a single pose based upon a consensus of scoring functions. Ligands are then scored and ranked with a number of structure-based or ligand-based scoring functions.

FRED was among the best and showed the lowest variability in its results of all the docking programs examined in an exhaustive study of virtual screening methods [2].

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

Features

• User-friendly graphical interface to set up the receptor file
• Directed docking with SMARTS patterns
• Systematic, exhaustive, nonstochastic docking for reproducible results at 30-40 molecules/minute
• Scoring functions: ChemScore, PBSA (ZAP), ChemGauss, PLP, ScreenScore
• Ligand-based scoring functions also available if bound ligand present
• Consensus structure: consensus pose selection for each ligand
• Refinement of docked poses in the context of the active site using MMFF94
• Multiple Active Site Corrections (MASC) for promiscuity [3]
• Distributed processing via PVM for most Unix platforms

For FRED and All OpenEye Products

• Multiple file format handling: robust reading and specification-compliant writing of: SMILES, SLN, SDF, MOL, MOL2, PDB, FASTA, MOPAC, MacroModel, XYZ, CCP4, XPLOR, and OEBinary.
• Platform independence: support for Linux, Windows, Mac OS X and many flavors of Unix in both 32 and 64 bit.

[1] McGann, M., Almond, H., Nicholls, A., Grant, J.A., and Brown, F., Biopolymers, 2003, 68, 76.
[2] McGaughey, G.B., Sheridan, R.P., Bayly, C.I., Culberson, J.C., Kreatsoulas, C., Lindsley, S., Maiorov, V., Truchon, J.-F. and Cornell W.D., J. Chem. Inf. Model., 2007, 47, 1504.
[3] Vigers, G.P., and Rizzi, J.P., J. Med. Chem., 2004, 47, 80.

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