ZINC database

Table 8.3 The VS performance of S VM and RF for FXa inhibitors against the MDDR database and the fragment-like subset of ZINC database...

Method The MDDR database The fragment-Kke subset of ZINC database ... 

Between these two developed LEVS models, the RF model is consistently superior to the SVM model (see Table 8.3). Thus, the developed RF model was employed as a more favorable model to identify the potential FXa inhibitors from the fragment-like subset of ZINC database, thereby resulting in 1211 potentially enriched hit candidates. The percent of the potentially enriched hits is 0.38 %, which can be comparable to other reported LEVS studies in screening large chemical libraries [26, 45, 56, 57],... 

Both search strategies reduced 3.7 M ZINC database compounds [29] to two candidate lists containing 51 and 49 compounds, respectively. After visual inspection... 

Figure 11.9 Practical selectivity searching. The diagram summarizes the results of selectivity searching for cathepsin K inhibitors, compound selection, and acquisition. As the compound database, a subset of the ZINC database was used [29].

The total chemical space is estimated as 10 ° distinct compounds (Mwt < 500 Da), although only 10 can be considered as drug-like and this set is composed of 10 different cores or scaffolds (Dean, 2007). From commercial sources, approximately 25 million compounds (ZINC database) (Irwin and Shoichet, 2005) are available although the diversity, particularly the skeletal diversity, is far behind what DOS strategy offers. On the... 

The given pharmacophore query is used to screen the molecules present in the ZINC database and gives the hits which can be downloaded. These screened compounds can be further validated through docking against the respective enzyme (Fig. 4.101). 

Fig. 4.101 Hits obtained after screening the ZINC database...

Table 5.1 shows the mean and standard deviations for the 2D measures employed here by looking at the distribution of similarity scores for 100,000 randomly chosen pairs of molecules from the ZINC database [25]. 

TABLE 5.1 Expectation Values and Standard Deviations of the Five Fingerprint Methods Used in This Study, Extracted from 100,000 Randomly Chosen Pairs from the ZINC Database... 

Expert-verified stmctures (26M rrrtique compourrds available as of Septerrrber 2013) and associated phy sico-cherrrical data trsing the Cherrrspider webportal [11] a list of 2.7M purchasable compormds can be fourtd in the ZINC database [12],... 

Fig. 2.5 MQN-nearest neighbour isomers of menthone (hit no. 1) in the ZINC database preserving the same number of H-bond donor atoms (0) and H-bond acceptor atoms (1)...

ADME/toxicity prediction, antipharmacophore, pharmacophore, elestrostatic similarity analysis, fingerprint diversity analysis 89,165 compounds from the natural product subset from ZINC database Partial 10 5 [30]... 

Another important contribution of virtual screening is generation of virtual screening databases for compounds like ZINC database at University of California San Francisco (Irwin and Shoichet 2005), and EDULISS at Edinburgh University (Taylor et al. 2008). Another large database. Chemical Universe Database GDB-13 follows different methods attempting to construct the universe of synthetic compounds (Blum and Reymond 2009). 

---