BioGem Blog

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 . B...

The three-dimensional (3D) structure of a compound can be retrieved using standard chemical nomenclature from the most popular databases, namely PubChem , ChEBI , ChEMBL , ChemSpider , CSD , ZINC , DrugBank , etc. If the 3D structure or chemical data is not available in the database, this simple tutorial helps you to predict the most optimal structure. The tools used in this tutorial are OPSIN (Open Parser for Systematic IUPAC Nomenclature), CACTUS , and Chimera .