In an evaluation published by Kontoyianni et. al [2], FlexX was used out of the box; for other programs in the test set, a very detailed listing of which parameters were used was given. Docking software, and FlexX is here no exception, requires careful inspection of the active site with subsequent adjustment of the receptor description (which for FlexX is contained in the receptor description file, rdf). Applying the default chemistry settings can certainly have disadvantageous effects on the result of the docking. This has to a lesser extent to do with a deep understanding of the software but rather a good understanding of the physico-chemical properties of the ligand and the binding site. We refer, as an example, to the adjustment of the degrees of freedom with respect to protonation/tautomers of amino acid residues.

Although results produced with FlexX look pretty encouraging in a publication by Chen et. al. [3], we noticed that the version of FlexX used (1.10.) was almost five years old at the time the paper was published. Even if one assumes a two year delay from the time of data generation until publication, the evaluation is still performed with software that was significantly older than its competitors.
To get the best out of FlexX, we encourage you to monitor the RSS feeds of our main and download web pages to automatically be informed about updates!
Another very important issue to be aware of is the definition of the binding site: For example, "applying a 10Å cut-off distance from the reference ligand". A common misperception is that the binding site is created from a single sphere around the reference ligand's center of mass. In fact, FlexX computes a 10Å sphere around each atom of the reference ligand, resulting in a larger binding site description than using a single sphere. Obviously, enlarging the search space will result in statistically larger RMSD values.
The proper definition of the binding site is just one of many critical parameters for the docking procedure.

Here is a short selection of further suggestions to consider in case you encounter problems with your FlexX docking:

if you encounter	then you could try analysis with	comments, flags, parameters for remedy
no or clashing solutions	ANALYZE/SCORE ref	Change MAX_OVERLAP_VOL or SOLUTIONS_PER_IT or LIGCLASH_HYDRO
base placement failure	PLACEBAS, LISTRMS or LISTSOL	Use MAPREF
placements not buried enough/ outside active site	DOCKING/MDRAW —> show all in FlexV	Use Release 2; Gaussian buriedness filters
bad solutions	LISTRMS or LISTSOL / FlexV	Check /Adjust rdf /amino acid template settings
badly docked large molecules	DOCKING/MDRAW —> show all in FlexV	Constrain amide bonds to planarity (see next newsletter)

Certainly, there are many more options to adjust in FlexX to better suit your needs. However, the program is so versatile so that we cannot go into all the details here. Then again: you can learn about all these things during our next FlexX docking workshop! Register, the next will be in September!

[1] J Cole, Comparing Protein-Ligand Docking Programs is Difficult Proteins 60, 325-332 (2005) [2] M Kontoyianni, Evaluation of Docking Performance: Comparative data on Docking Algorithms J. Med. Chem. 47, 558-565 (2004) [3] H Chen, On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors J. Chem. Inf. Model. 46, 401-415 (2006)