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Comparison of the docking model with the crystal structure recently obtained for a trimmed version of the complex reveals the high accuracy of the docking model, even down to an atomic level.

The docking model with the lowest binding energy was selected and visualized.

Briefly, in 30 of the 33 cases where there were at least two predicted contacts with scores greater than 0.6, the docking model with the best gremlin score was within 2 Å RMSD of the experimentally determined complex structure.

The docking experiment was then performed with the AutoDockVina software (Trott and Olson, 2010), and the docking model with the lowest binding energy (expressed in kcal per mol) was selected and visualized in the Chimera software (Pettersen et al., 2004).

The docking score for tricetin ranged between -19.03 and -12.48, and the docking model with a score of -15.71 was fitted to the binding site and used in this study.

For each level of receptor, we compared results based upon the "sharing" docking model with results generated using a "competing" docking model.

Based on the information obtained from a docking model with androgen receptor (AR), we modified a hit compound A identified through high-throughput screening.

DOI: http://dx.doi.org/10.7554/eLife.00857.036 The docked compounds were filtered based on the following criteria: (1) The docking models with a compound-fiber van der Waals attractive energy > −7.0 kcal/mol were removed; (2) The docking models with a compound-fiber hydrogen-binding energy >−0.2 kcal/mol were eliminated.

A theoretical docking model, consistent with the experimental observations, is presented.

As shown in Table 1, four docking models with significant levels of docking energy were identified.

(A – C ) The docking model of the ectodomain with chitooctaose shown in surface (A ) and ribbon form (B ) and a close-up surface (C ).