DOCK/PMF

Figure 6 Ranking list of 3247 compounds with an average molecular weight (MW) of 191 Da (left) and a subset of 2077 compounds with MW < 210 Da (right) according to their best scores in a DOCK/PMF run against FK506 binding protein. Computational ranks for the active compounds in the database are marked with horizontal bars. Data are taken from Muegge et al. (Ref. 45). Bold bars depict close neighboring bars.

Figure 8 Crystal structure of BANA113 bound to influenza virus neuraminidase. Docked conformations ranking first (correct) and eleventh (incorrect) in a DOCK/PMF score docking experiment are compared to the crystallographic binding mode.

Ha et al. [150] have shown that DOCK/PMF predicted scores correlate significantly with the measured binding affinities for the highest scoring binding modes of 61 stromelysin/inhibitor complexes [150]. 

The calculation of the binding affinity with con.sidcration of all tbc.se effects for virtual screening is not possible. In order to circumvent thus difficulty, scoring functions arc used instead, c.g., the Liidi scoring function [80, or consensus scoring functions derived from FlevX score, DOCK score, GOLD score, ChemScore, or PMF score [81 ]. 

File (in spreadsheet) > Put Rows into Molecule Areas Alternatively, if one has access to the CSCORE module of SYBYL, one can calculate scores of FlexX (50), Gold (38), PMF (51), Dock (52), and Chem-score (53) with a previously saved table of docked conformations. First, the table (corresponding to the database containing the conformations) is loaded File > Molecular Spreadsheet > New > Database (and select the database)... 

Chemscore Cscore Regression-based scoring function Suite of scoring functions (ChemScore, DOCK, FlexX, GOLD, PMF) and consensus scoring tool... 

Evaluation of PMF Scoring in Docking Weak Ligands to the FK506 Binding Protein. 

Muegge I, Martin YC, Hajduk PJ, Fesik SW. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem 1999 42 2498-503. 

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