: An accessible cheminformatics platform for similarity operations on chemicals datasets

Himaghna Bhattacharjee, Jackson W. Burns, Dionisios G. Vlachos

Abstract: The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a Graphical User Interface for code-free utilization with fully interactive plots.Program summaryProgram title: AIMSimCPC Library link to program files: https://doi.org/10.17632/ydbmr9v3g3.1Developer's repository link: https://github.com/VlachosGroup/AIMSimLicensing provisions: MIT licenseProgramming language: PythonExternal routines: NumPy, Pandas, Matplotlib, RDKit, Plotly, Scikit-learn, Seaborn, Mordred, PyYAML, Padelpy, Scipy, Tabulate.Nature of problem: Calculating and visualizing structural similarity between chemical entities is challenging and has a wide variety of approaches based on niche applications. An accessible tool which unifies these cheminformatics operations is lacking.Solution method: Python package with a modular, flexible, and interactive approach to molecular fingerprinting, clustering, and more advanced cheminformatics operations. Includes a Graphic User Interface (GUI) for completely code-free utilization.