Extending Chemoinformatics Techniques With JMolecular Energy: A Robust CDK-Based Force Field Library

Abstract

Computational chemistry plays a crucial role in drug design and development, where accurate modeling of molecular interactions is vital in rational drug design. Among the available methods, force fields such as MMFF94 are extensively used to calculate molecular potential energies, especially for small organic molecules. However, current implementations of MMFF94 are primarily available in commercial software or as closed-source modules. Open-source packages often offer limited functionality and lack extensibility. This paper introduces JMolecular Energy (JME), a novel, open-source Java library designed to implement MMFF94 with a robust and extendable API (Application Programming Interface) that allows for access to individual energy components. Leveraging the Chemistry Development Kit (CDK), JME provides a modular framework for potential energy calculation and facilitates functionalities previously absent in CDK, such as 3D conformation energy minimization. Additionally, JME establishes a framework for tailoring force field energy terms for various applications and facilitates the integration of custom-built force fields.