How to bind a selectOneChoice component to a relationship field when using ADF with JPA

We report unrestrained, all-atom molecular dynamics simulations of HIV-1 protease (HIV-PR) with a continuum solvent model that reproducibly sample closing of the active site flaps following manual placement of a cyclic urea inhibitor into the substrate binding site of the open protease. The open form was obtained from the unbound, semi-open HIV-PR crystal structure, which we recently reported (Hornak, V.; et al. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 915-920.) to have spontaneously opened during unrestrained dynamics. In those simulations, the transiently open flaps always returned to the semi-open form that is observed in all crystal structures of the free protease. Here, we show that manual docking of the inhibitor reproducibly induces spontaneous conversion to the closed form as seen in all inhibitor-bound HIV-PR crystal structures. These simulations reproduced not only the greater degree of flap closure, but also the striking difference in flap "handedness" between bound and free enzyme. In most of the simulations, the final structures were highly accurate. Root-mean-square deviations (RMSD) from the crystal structure of the complex were ~1.5 Å (averaged over the last 100 ps) for the inhibitor and each flap despite initial RMSD of 2-5 Å for the inhibitors and 6-11 Å for the flaps. Key hydrogen bonds were formed between the flap tips and between flaps and inhibitor that match those seen in the crystal structure. The results demonstrate that all-atom simulations have the ability to significantly improve poorly docked ligand conformations and reproduce large-scale receptor conformational changes that occur upon binding.

Observers often pair colours with earlier periods of motion. This observation has prompted the proposal that changes in colour are processed faster and perceived as occurring before physically coincident changes in direction—a brain-time account. Alternatively, it has been proposed that the sudden onset of a surface, or a direction reversal within a persistent surface, can trigger an analysis that determines the perceptual properties of the surface. Hypothetically, this analysis persists for some period of time and the consequences are perceived as having occurred when the analysis commenced—a post-dictive account. Hypotheses based upon these alternate accounts are contrasted in a series of experiments. It is shown that the optimal conditions for pairing specific combinations of colour and motion arise when colour changes are delayed relative to direction changes. In these conditions observers can pair more rapid oscillations of colour and motion and perceptual pairings are more systematic relative to when the changes in colour and direction are physically synchronous. It is also shown that, when pairing colour and motion, the sudden onset of a moving surface does not have the same consequences as a direction reversal within a persistent surface. These findings are consistent with the brain-time, but are inconsistent with the post-dictive, account of perceptual asynchrony.

The brain processes distinct attributes such as colour and motion in anatomically largely segregated systems. Moreover, these two attributes are perceived with different latencies. Here, we show that the time required to bind these two attributes differs too. In psychophysical experiments, we determined minimal presentation times required to perceptually pair spatially separate pairs of stimuli consisting of colour or motion. Binding two colours required longer presentation times than binding the directions of two moving stimuli. Cross-attribute binding between colour and motion took longer than within-attribute binding. This was so even when the relative perceptual delay between colour and motion was compensated for, which accelerated colour–motion binding. Moreover, stimuli could be discriminated but not bound at fast presentation rates. Our results thus show that spatial binding is an attribute-specific process and faster within the same than across different attributes. Furthermore, the time required to bind attributes is independent of that required to process them, since colour is perceived before motion but requires longer time for binding. Finally, our results suggest that binding acts on attribute-specific neural representations of the stimuli at a late, perceptually explicit stage. These results lead us to conclude that spatial binding is separate from, and subsequent to, stimulus processing and that it is an attribute-dependent and post-conscious process.