3.3 Results on The Gold Test Set

Included in the flynn distribution is a copy of the proteinligand complexes that have structures factors available from the Electron Density Server[21].

Along with this data set is a simple python script that can be used to fit ligands to the test data set. OpenEye has prepared the input test set as follows:

The Structure Factors and protein complexes were downloaded from EDS.
The ligands were separated from the proteins.
The protein was rerefined using the original mtz file to remove ligand bias.

A simple directory structure was created as follows:

pdbcode $\backslash$ protein.pdb - the re-refined protein
pdbcode $\backslash$ ligand.pdb - the original ligand
pdbcode $\backslash$ protein.mtz - the re-refined difference map density.

The following python script was used to run flynn on all of the proteins. (This script is also included in the flynn distribution)

#########################################################################################
## Copywrite (C) OpenEye Scientific 2008
#########################################################################################
## This script analyzes the Gold dataset shipped with the flynn distribution

import os,sys

command = "../../../bin/flynn -in %(CODE)s/ligand.pdb -map %(CODE)s/protein.mtz " \
          "-prot %(CODE)s/protein.pdb -out %(CODE)s_results.sdf " \
          "-verbose -rms -reportfile %(CODE)s.log %(REDIRECT)s %(CODE)s.out"

if sys.platform == "win32":
   REDIRECT = "2>"
else:
   REDIRECT = "&>"

RMS = []
for file in os.listdir("."):
    print file
    if os.path.isdir(file) and len(file) == 4:
        code = file
        CMD = command % {"CODE":code, "REDIRECT": REDIRECT}
        print CMD
        os.system(CMD)

        index = None
        rmses = []
        for line in open("%s.log"%code):
           if index is None:
              index = line.strip().split(",").index("RMSD")
           else:
              rmses.append( float(line.strip().split(",")[index]) )
        if rmses:
            print "\t===>Lowest RMS", min(rmses)

The results of flynn are shown in Figure 3.1. The mean RMS to the crystal structure is 0.676 angstroms.

**Figure 3.1:** Gold Test Set Results

Note that flynn could not fit one of the ligands in the Gold test set, namely 1VGC as this molecule contained a boron atom and the MMFF94 force field is not parameterized for this atom type. Replacing the boron with a phosphorous gave an RMS of 0.54 angstroms to the crystal structure but this type of atomic replacement, while possible in a pinch, is suspect.

				FLYNN

				FLYNN