Generating 3D Structure Offline using JSME and BALLOON


JME/JSME is a free and open-source molecule editor developed by Peter Ertl and Bruno Bienfait. JSME (JavaScript Molecule Editor) is the successor of JME (Java Molecule Editor). JME is a Java applet application converted to JavaScript due to security and portability issues in Java. JSME is a popular lightweight molecule editor application developed so far.

Jmol/JSmol is a free and open-source molecule visualization tool developed by Bob Hanson. JSmol (JavaScript Molecule Viewer) is the successor of Jmol (Java Molecule Viewer). Jmol is a JAR (Java ARchive) application converted to JavaScript due to security and portability issues in Java. Jmol is the most popular molecule visualization tool implemented in many bioinformatics or cheminformatics web applications.

JSmol in collaboration with JSME, has implemented a 2D (SMILES string) to 3D structure conversion method by integrating the API of the CACTUS server. The link to an interactive demo of JSME and JSmol is here.

JSME with JSmol

BALLOON is a free command-line program for 3D molecular model generation and conformational analysis developed by Mikko Vainio. It runs on any platform/operating system for which a binary executable has provided. BALLOON creates 3D atomic coordinates from molecular connectivity via distance geometry and conformer ensembles using multi-objective genetic algorithm. It uses MMFF94-type non-polarizable charges and polarizable (conformation-dependent) electronegativity equalization charges (SFKEEM and EEM) for performing geometry optimization. This is a simple video tutorial to build a 3D small molecule by drawing its 2D chemical structure using JSME Molecule Editor and the BALLOON tool.


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