IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding
Citations
634 citations
Cites background or methods from "IC50-to-Ki: a web-based tool for co..."
...IC50 depends on the concentration of the target and ligand (Cer et al., 2009) and low IC50 values signal strong binding....
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...lly expressed in measures such as dissociation constant (Kd), inhibition constant (Ki), or the half maximal inhibitory concentration (IC50). IC50 depends on the concentration of the target and ligand [8] and low IC50 values signal strong binding. Similarly, low Ki values indicate high binding affinity. Kd and Ki values are usually represented in terms of pKd or pKi, the negative logarithm of the diss...
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...s we performed a search over [16, 32, 64, 128, 512]. We then narrowed the search range around the best performing parameter (e.g. if 16 was chosen as the best parameter, then our range was updated as [4, 8, 16, 20] etc.). As explained in the Proposed Model subsection, the second convolution layer was set to contain twice the number of filters of the first layer, and the third one was set to contain three times ...
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... that were used for the compound CNN-block and protein CNN-block. Table 2. Parameter settings for CNN based DeepDTA model Parameters Range Number of filters 32*1; 32*2; 32*3 Filter length (compounds) [4,6,8] Filter length (proteins) [4,8,12] epoch 100 hidden neurons 1024; 1024; 512 batch size 256 dropout 0.1 optimizer Adam learning rate (lr) 0.001 In order to provide a more robust performance measure, we...
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359 citations
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Cites methods from "IC50-to-Ki: a web-based tool for co..."
...Recently, two groups have incorporated derivations of Ki/Kd from IC50 data, including FP results, into web-based algorithm tools [16-19]....
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278 citations
References
12,583 citations
"IC50-to-Ki: a web-based tool for co..." refers background in this paper
...protein)-binding studies, the free concentrations also become sufficiently important to require modifications of these equations (1, 2), and (9)....
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507 citations
"IC50-to-Ki: a web-based tool for co..." refers background or methods in this paper
...protein)-binding studies, the free concentrations also become sufficiently important to require modifications of these equations (1, 2), and (9)....
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...The website cited in (9) served as an initial design template for our IC50-to-Ki converter....
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...(3), (6) and (9) whereas we derived Equation (5) for this study....
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486 citations
455 citations
"IC50-to-Ki: a web-based tool for co..." refers methods in this paper
...Experimental data (IC50 values) and accompanying assay information were manually extracted from primary literature results and other relevant databases: JCVIPathema-Clostridium (13), Brenda (14) and Protein Data Bank (15)....
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177 citations