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ed to be used as PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19667117 benchmark to assess the quality enhancements by using the FFR model of InhA (20,000 snapshots). Overall, crossdocking experiments present FEB values close and, for some ligands, higher than redocking experiments, as in the case of TCL300, 566, 5PP, 8PS, PTH-NAD, THT and INH-NAD. In addition to FEB, we also considered the RMSD values. This index verifies whether docking parameters specified in the input file are capable of reproducing the interaction and the Table 2. Summary of docking experiments performed to analyze the clustering results. Table 2 highlights the RMSD values for 665, 468, 641, 744, 8PS, and GEQ since these ligands present energetically favorable interactions with the MD trajectory, but their final binding-mode are significantly different from those obtained by the crystallographic structures. It is worth notice that the FEB and RMSD values from Table 2 show that ligands resulting from adducts of NADH fit better in the FFR model than their crystallographic structures. For instance, RMSD values from the lowest energy conformation for INH-NAD and PTH-NAD ligands are around 0.8 � in cross-docking experiments and over 1.9 � in redocking experiments. This well fit is justified by the fact that the FFR model was generated from an MD simulation of BQ-123 web 19666694″ title=View Abstract(s)”>PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19666694 the InhA-NADH enzyme complex, which in turn provides suitable clefts in the substrate-binding cavity due to its flexibility. Remaining ligands were unable to overcome RMSD values undertaken by crystallographic structures but they present very similar FEB values. It means that, the FFR model of 1ENY was able to produce a favorable interaction with the ligands even when the RMSD is higher than the crystallographic conformation. In this study, we omitted d