Seeding experiments

Seeding experiments allow for comparisons of different scoring functions with respect to their performance for different targets. Seeding experiments 

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Wayne Genck (7 8) has recently published several useful articles about batch crystallization. Often lab filtration after crystallization is done with a thin cake and no problem is observed. But when taken to the plant, this operation takes days to build and wash a cake. To avoid this problem it is best to operate a crystallizer that is properly seeded and cooled according to a profile that follows the equation in reference (7), slow at first and fastest at the end. The other reference (8) discusses the challenges without seeding. Experience by the author confirms that a large amount of seed crystal is required, about 1-2 % wt of the final crystal yield. 

Another aspect of the seeding experiment is that it provides us with important information on the particle growth mechanism, as mentioned in Section 1.3 in Chapter 1. The total reaction for the formation of the BAS particles is greatly accelerated... 

Each experiment is performed at one of two levels of each factor, just as for the two-level factorial designs described above. The contrast coefficients are a consequence of by the method and are generated from the conditions of a seed experiment by advancing each designated level around the fac-... 

To probe the self-replicating properties of the system, seeding experiments were performed by adding either preformed hexamer or heptamer to solutions of 1 which were then respectively shaken or stirred for several days. The results clearly indicated the induced formation of the corresponding macrocyles. In addition, the solutions of both hexamer and heptamer were characterized by cryo-TEM revealing the presence of 1-2 pm length fibers with diameters in the range of 4.7 1.9 nm... 

Figure 4 Results of a seeding experiment. The ranks of known p38 MAP kinase inhibitors are shown as horizontal lines in the four diagrams. Inhibitors have been divided into two classes those forming one or two hydrogen bonds to the p38 MAP kinase ATP binding site. The FlexX scoring function preferentially enriches those inhibitors that form two hydrogen bonds. This tendency is less pronounced for the PLP scoring function. The inhibitors with the best predicted affinities are at the top. Data is shown for the top 300 compounds in terms of docking scores.

Figure 5 Results of seeding experiments on two targets with three different scoring functions. In both graphs, the accumulated percentages of active compounds are plotted against the percentage of the total ranked library. The smooth exponential curve in each graph corresponds to the hypothetical case of no enrichment and assumes a random ordering of the database.

Seeding Experiments to Assess Docking and Scoring in Virtual Screening, 318... 

Several seeding experiments have been published. An example has been performed at Merck using FLOG (121). A library consisting of 10,000 compounds including inhibitors cf various types of proteases and HIV protease was docked into the active site of HIV protease. This resulted in excellent enrichment of the HIV protease inhibitors all inhibitors but one were among the top 500 library members. However, inhibitors of other proteases were also considerably enriched (366). 

The stationary layer thickness (i ) has to be much larger than the particle size. Usually, d is believed to he on the order of 10 fan, decreasing with increasing stirring intensity. For particles in the nucleation range (2-20 nm) this condition is very well fulfilled for seeded experiments with larger particles the assumption may be doubtful. 

The ideal seeded experiment would be where seed latex particles are prepered in which the MWD of the seed is significantly different from that formed during subsequent seeded polym tzation. The instantaneous MWD formed at early times could then be estimated directly. Seed latexes of different sizes could be used to probe the effect of compartmentalization we Stress again that if the system is transfer-dominated, the MWD of formed polymer should be independent of panicle size). 

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