Similarity threshold

Figure 9. Potential energy diagram (in kJ mol ) showing energetically allowed photodissociation channels for CH3CHO. Note the similar threshold energies for the four energetically allowed channels. Reprinted with permission from Dr. Scott Kable, University of Sydney.

In the detection of repeats using SMART an algorithm is used that derives similarity thresholds that are dependent on the number of repeats already found in a protein sequence (Andrade et al., 1999b). These thresholds are based on the assumption that suboptimal local alignment scores of a profile/HMM against a random sequence database are well described by an extreme value distribution (EVD). The result of this protocol is that acceptance thresholds for suboptimal alignments are lowered below the optimal scores of nonhomologous sequences. 

Several other approaches with the goal of simultaneous optimization of several criteria have been reported. One such approach is the generation of a library that is both focused and diverse via the dual fingerprint metric described by Bajorath [94], In this method, individual compounds are randomly generated and their similarity to a known inhibitor is evaluated by comparison of their minifingerprints [95] using the Tanimoto coefficient. Those molecules that are above a similarity threshold are then... 

Given a set of molecules known to be inside PGVL as query molecules, what is the success rate for returning the expected molecules identical to the query molecules (100% similarity threshold) This is by definition a baseline test that a validated search strategy must pass. 

Similarity threshold No of cpds retrieved by LEAP1 retrieved by exhaustive search No of true positives in LEAP1 % true positive in LEAP1 No of false negatives in LEAP1 % false negative in LEAP1... 

In the second example, LEAP2 was utilized to help generate novel leads against an anti-angiogenesis target, caspase-3 (29, 30). A literature compound (PAC-1 with reported 3.1 xM IC50) and five of its analogs (31) were used as query molecules, and the product similarity threshold was set as top 50 final output molecules... 

Fig. 4.14 Search results for three different targets. Whereas hits close to the query could be retrieved with a high similarity value (not shown), at a lower similarity threshold so-called plausible hits were retrieved which are close to actives for the same tar-...

Size of test system causes significant differences in fate and, therefore, exposure concentrations. However, where exposure regimens are similar, threshold concentrations for similar effects in different types of test systems also are similar, at least when they contain enough representatives of sensitive taxonomic groups. The extrapolation of NOECecosystemvalues from one system to another is possible with lower uncertainty than in hazard estimates of higher concentrations in which both direct and indirect effects and recovery processes are involved. 

To summarize, studies of differently thermally adapted confamilial, congeneric, and con-specific organisms have shown that temperature differences of a few degrees Celsius have sufficient effects on proteins to favor adaptive change. Although studies to date have focused on only a few classes of proteins, the ubiquitous effects of temperature on protein conformation are such that many, and perhaps most, proteins are likely to exhibit a similar threshold for perturbation and adaptive change. 

Double-walled carbon nanotubes (DWNTs), first observed in 1996, constitute a unique family of carbon nanotubes (CNTs). -2 DWNTs occupy a position between the single-walled carbon nanotubes (SWNTs) and the multiwalled carbon nanotubes (MWNTs), as they consist of two concentric cylinders of rolled graphene. DWNTs possess useful electrical and mechanical properties with potential applications. Thus, DWNTs and SWNTs have similar threshold voltages in field electron emission, but the DWNTs exhibit longer lifetimes.3 Unlike SWNTs, which get modified structurally and electronically upon functionalization, chemical functionalization of DWNTs surfaces would lead to novel carbon nanotube materials where the inner tubes are intact. The stability of DWNTs is controlled by the spacing of the inner and outer layers but not by the chirality of the tubes 4 therefore, one obtains a mixture of DWNTs with varying diameters and chirality indices of the inner and outer tubes. DWNTs have been prepared by several techniques, such as arc discharge5 and chemical vapor depo-... 

Nielsen, H Engelbrecht, J., von Heijne, G. Brunak, S. (1996). Defining a similarity threshold for a functional protein sequence pattern the signal peptide cleavage site. Proteins 24,165-77. (The data set is available from the FTP server at ftp //virus.cbs.dm.dk/pub/signalp). 

It turned out that the states and provinces had more in common than not, with similar thresholds for notifying neighbors, though the tools might differ. For example, Canadians use a system called CIOSC to send epidemiological alerts. Health officials in the states use... 

The similarity threshold for ligand pairs that are considered in calculating the discontinuity score is set to 0.6. This relatively soft threshold value ensures that also potency differences between remotely similar compounds are taken into account and thus enables a thorough assessment of putative activity cliffs, which is further emphasized by multiplication by pair-wise ligand similarity. 

Peukert et al. (2010a) propose the use of filter operators within match work-flows to prune dissimilar element pairs (whose similarity is below some minimal threshold) from intermediate match results. The threshold is either statically predetermined or dynamically derived from the similarity threshold used in the match workflow to finally select match correspondences. Peukert et al. (2010a) also propose a rule-based approach to rewrite match workflows for improved efficiency, particularly to place filter operators within sequences of matchers. 

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