Nearest-neighbor lists

The second stage scans the nearest-neighbor lists to create clusters that fulfill the three following neighborhood conditions ... 

To scan the nearest-neighbor lists and create the clusters in this stage of nonhierarchical clustering, the following three steps are carried out ... 

For each pair of compounds, i and j (i < j), compare the nearest-neighbor lists on the basis of the three neighborhood conditions. If the three conditions are passed, replace the cluster label for compound j with the cluster label for compound i. Then, scan all previously processed compounds and replace any occurrences of the cluster label for compound j by the cluster label for compound i. 

Jarvis-Patrick clustering requires a nearest-neighbor list. The rms matrix is treated as an N-dimensional Cartesian coordinate matrix for N conformers... 

Data fusion can be performed in a number of ways. Most often used are the MIN, MAX, and SUM rules. According to these rules, the minimum or maximum score value or the sum of the scores is taken from a list of different similarity values for a compound that result from different virtual screening runs. It was also recommended to consider only the ranks of the compound in the corresponding nearest-neighbor lists [51]. Hert et al. [41] observed the superiority of the SUM rule when fusion is performed on ranks, whereas the MAX rule gives better results if the fusion is performed on scores, which is in line with earlier results from Schuffenhauer et al. [52]. Whittle et al. [50] observed a superiority of the MAX rule over the SUM rule for group fusion. 

In essence, the chance to find active compounds is higher if they are detected by more than one descriptor. On the other hand, by concentrating only on compounds that are detected by several methods, a lot of valid actives vdll be missed. Therefore, the authors prefer to simply merge the nearest-neighbor lists of different virtual screening methods and reference structures, respectively. 

Whittle M, Gillet VJ, Willett P, Alex A, Loesel J (2004) Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists a comparison of similarity coefficients. J Chem Inf Comput Sci 44 1840-1848... 

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