In the era of antibiotic resistance, in silico prediction of bacterial resistome profiles, likely to be associated with inactivation of new potential antibiotics is of utmost importance. Despite this, to the best of our knowledge, no tool exists for such prediction. Therefore, under the rationale that drugs with similar structures have similar resistome profiles, we developed two models, a deterministic model and a stochastic model, to predict the bacterial resistome likely to neutralize uncharacterized but potential chemical structures. The current version of the tool involves the prediction of a resistome for Escherichia coli and Pseudomonas aeruginosa. The deterministic model on omitting two diverse but relatively less characterized drug classes, polyketides and polypeptides showed an accuracy of 87%, a sensitivity of 85%, and a precision of 89%, whereas the stochastic model predicted antibiotic classes of the test set compounds with an accuracy of 72%, a sensitivity of 75%, and a precision of 83%. The models have been implemented in both a standalone package and an online server, uCAREChemSuiteCLI and uCARE Chem Suite, respectively. In addition to resistome prediction, the online version of the suite enables the user to visualize the chemical structure, classify compounds in 19 predefined drug classes, perform pairwise alignment, and cluster with database compounds using a graphical user interface.

Availability

uCARE Chem Suite can be browsed at: https://sauravsaha.shinyapps.io/ucarechemsuite2/, and uCAREChemSuiteCLI can be installed from:

1. CRAN (https://cran.r-project.org/package=uCAREChemSuiteCLI) and

2. GitHub (https://github.com/sauravbsaha/uCAREChemSuiteCLI).

中文翻译：

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uCARE Chem Suite 和 uCAREChemSuiteCLI：细菌耐药组预测工具

在抗生素耐药性时代，对可能与新的潜在抗生素失活有关的细菌耐药组谱的计算机预测至关重要。尽管如此，据我们所知，不存在用于此类预测的工具。因此，在具有相似结构的药物具有相似的抗性组谱的基本原理下，我们开发了两个模型，一个确定性模型和一个随机模型，以预测可能中和未表征但潜在的化学结构的细菌抗性组。该工具的当前版本涉及预测大肠杆菌和铜绿假单胞菌的抗性组。省略两种不同但特征相对较少的药物类别聚酮化合物和多肽的确定性模型显示出 87% 的准确度、85% 的灵敏度和 89% 的精确度，而随机模型预测测试集化合物的抗生素类别准确度为 72%，灵敏度为 75%，精密度为 83%。这些模型分别在独立软件包和在线服务器 uCAREChemSuiteCLI 和 uCARE Chem Suite 中实现。除了抗性组预测外，该套件的在线版本还使用户能够可视化化学结构、将化合物分类为 19 种预定义药物类别、执行成对比对以及使用图形用户界面与数据库化合物进行聚类。

可用性

uCARE Chem Suite 可以在以下位置浏览：https://sauravsaha.shinyapps.io/ucarechemsuite2/，uCAREChemSuiteCLI 可以从以下位置安装：

1. CRAN (https://cran.r-project.org/package=uCAREChemSuiteCLI) 和

2. GitHub (https://github.com/sauravbsaha/uCAREChemSuiteCLI)。