A tool written in Scala for preparation and analysis in MD simulation and 3D-RISM calculation of biomolecules

Abstract

Researchers studying biomolecules require easy-to-use, customizable tools allowing them to effectively use other molecular science packages written for molecular dynamics (MD), quantum chemistry, statistical mechanics, and molecular graphics. This paper presents a Scala tool for the computational science of biomolecules (STCSB) developed in Scala, which allows users to prepare and run MD simulations, as well as perform three-dimensional reference interaction site model (3D-RISM) calculations of biomolecules. Features of the STCSB include the following: (1) a cross-platform application running on a Java virtual machine; (2) handling hierarchical XML-based data formats such as the protein data bank markup language (PDBML); (3) prepared application programming interfaces (APIs) with both character user interface (CUI) and graphical user interface (GUI) options; (4) prepared APIs for molecular graphics; and (5) a scalable source code based on the Model-View-Controller (MVC) architectural pattern.