## Wednesday, July 26, 2006

### Test of methods

• Reassembling Complexes: generation of the experimental structure of the complex as the best scoring geometry.

$Rmsd = \sqrt{\frac{\sum_{i=1}^{N_{a t o ms}} d_{i}^2}{N_{a t o ms}}$

$d_i$ is the distance between the coordinates of atoms i in the two structures when overlaid. Generally less than 2 Amstrongs is considered acceptable for small ligands.

Several algorithms have been proposed for incorporating flexible receptor information. Rmsd may not be the best metric for systems that exhibit conformational changes. It is important to know how robust the geometry is to changes in ligand or changes (mutations) in the receptor.

• Rank ordering of energies: a docking program can do this rank. It is used in both library screening and lead optimization. The challenge is to rank correctly ligands that are very similar to each other. An improvement is to use consensus scoring.
• Virtual Screening: two metrics are used: hit rate and the enrichment factor (number of TP divided by number of TP+FP).
• Common Docking Failures: incomplete searching and innacurate scoring function. Algorithm or soft failure: probably due to the rugged, multiminima character of the binding energy landscapes. Scoring or hard failure: when the crystal structure has a higher energy than the predicted.

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