![]() ![]() However, it has advantages and limitations that are similar to those of ChemoPy. (As described later, this disadvantage can be overcome by using several web interfaces that incorporate ChemoPy.) To date, ChemoPy only supports Python 2.įurthermore, PyDPI can calculate small molecule descriptors as well as protein descriptors. However, it can be difficult to employ it by non-Python users who are not familiar with the construction of the Python interface. ChemoPy is available as a Python package and is convenient for constructing models using Python machine-learning packages. ChemoPy, a free software environment that calculates both 2D and 3D descriptors, can calculate 1135 descriptors. However, BlueDesc can calculate only 174 descriptors, and it has no configurable options. ![]() Because BlueDesc can output the results in libSVM input file format, users can easily construct SVM models. Meanwhile, BlueDesc is a simple software program for calculating descriptors. However, we determined that it has several defects (Table 2), which implies that careful verifications and modifications are required when using it. Thus, these advantages make it one of the best choices among open-source molecular-descriptor calculators. Moreover, it can calculate descriptors in parallel. It provides several interfaces (e.g., a graphical user interface (GUI), command line interface (CLI), Konstanz Information Miner (KNIME), and Rapid Miner ), and it has been cited by other papers more than 300 times. The freely available PaDEL-Descriptor can calculate 1875 molecular descriptors and fingerprints. Split the dataset into training and test datasets for evaluating the predicted performance of the model.Ĭalculate numerous molecular descriptors of each compound in the datasets.Ĭonstruct a reliable model of the training dataset to predict the target activity or property from these calculated descriptors using classification or regression methods (e.g., multiple regression analysis, partial least squares regression, support vector machine (SVM), and random forest).Įvaluate the performance of the constructed model by predicting the target activities of the compounds in the test dataset that are not used for model construction.Īlthough both open-source and proprietary software have been developed for calculating molecular descriptors-such as PaDEL-Descriptor, BlueDesc, ChemoPy, PyDPI, Rcpi, cinfony, and Dragon -they each have advantages and disadvantages (Table 1). The steps in a general procedure of QSPR model construction using molecular descriptors are outlined below. They are studied to predict the activity, toxicity, and other properties resulting from the chemical structures of compounds. Quantitative structure–property relationship (QSPR) models frequently use molecular descriptors. Many types of molecular descriptors have been developed, such as the number of carbon atoms molecular weight predictive values of LogP (XLogP, ALogP, etc.) properties calculated from two-dimensional (2D) structures (e.g., Eccentric Connectivity Index ) and three-dimensional (3D) structures (e.g., charged partial surface area (CPSA) ) and properties based on quantum mechanics (orbital energies of highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), etc.). Owing to its good performance, convenience, number of descriptors, and a lax licensing constraint, Mordred is a promising choice of molecular descriptor calculation software that can be utilized for cheminformatics studies, such as those on quantitative structure–property relationships.Ī molecular descriptor is defined as the “final result of a logical and mathematical procedure, which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment”. ![]() Performance benchmark results show that Mordred is at least twice as fast as the well-known PaDEL-Descriptor and it can calculate descriptors for large molecules, which cannot be accomplished by other software. Mordred can be easily installed and used in the command line interface, as a web application, or as a high-flexibility Python package on all major platforms (Windows, Linux, and macOS). ![]() To address these issues, we propose Mordred, a developed descriptor-calculation software application that can calculate more than 1800 two- and three-dimensional descriptors. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. Various molecular-descriptor-calculation software programs have been developed. Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. ![]()
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