Molecular editor

• Main Author: Heng, Xiu Ting
• Other Authors: Kwoh Chee Keong
• Format: Final Year Project
• Language: English
• Published: 2015
• Subjects: DRNTU::Engineering::Computer science and engineering::Software
• Online Access: http://hdl.handle.net/10356/62895
• Institution: Nanyang Technological University

Chemist and drug design specialists are involved in the synthesis and development of new pharmaceutical drugs. Traditional methods of drug discovery relied on trial-and-error testing on animals or cultured cells to check the effectiveness of the drug. As technology develops, computer-aided tools became more commonly used in helping drug design and study of drugs. This project was designed to develop a desktop Graphical User Interface (GUI) application that helps these chemist and drug design specialist to handle the molecules easily. The application enables users to read and modify molecules read from Protein Data Bank (PDB) file format. Users are able to modify molecules such as select, delete, copy, cut and paste of atoms. After modification of the molecules, the application is able to calculate and minimize the molecular internal energy for users to study the new molecules. The application uses Steepest Descent Energy Minimization and Merck Molecular Force Field (MMFF94) to calculate energy minimization. It uses the minimization method from Jmol’s minimize package as reference for the implementation of energy minimization. However, there is presence of disparity between the energy values calculated from Jmol and this application. A possible source of difference could be due to the sequence of computation of the molecule. This paper documents the design and implementation of the application of completed features such as reading data files for display and manipulation of the molecules and energy minimization of the molecule. It also includes the data for energy minimization of test models and discussion of the results of manipulation of model and energy minimization. The paper ends with the conclusion and future improvements to the project.