SWIFT MODELLER: A JAVA based GUI for molecular modeling

• Published in: Journal of molecular modeling Vol. 17; no. 10; pp. 2601 - 2607
• Main Authors: Mathur, Abhinav, Shankaracharya, Vidyarthi, Ambarish S.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.10.2011
• Subjects: Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Computer Graphics; Models, Molecular; Molecular Medicine; Original Paper; Programming Languages; Theoretical and Computational Chemistry; User-Computer Interface; MODELLER; Molecular modeling; Loop modeling
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-011-0960-4

MODELLER is command line argument based software which requires tedious formatting of inputs and writing of Python scripts which most people are not comfortable with. Also the visualization of output becomes cumbersome due to verbose files. This makes the whole software protocol very complex and requires extensive study of MODELLER manuals and tutorials. Here we describe SWIFT MODELLER , a GUI that automates formatting, scripting and data extraction processes and present it in an interactive way making MODELLER much easier to use than before. The screens in SWIFT MODELLER are designed keeping homology modeling in mind and their flow is a depiction of its steps. It eliminates the formatting of inputs, scripting processes and analysis of verbose output files through automation and makes pasting of the target sequence as the only prerequisite. Jmol (3D structure visualization tool) has been integrated into the GUI which opens and demonstrates the protein data bank files created by the MODELLER software. All files required and created by the software are saved in a folder named after the work instance’s date and time of execution. SWIFT MODELLER lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with.