Combined Knowledge And Physics Based Approaches Towards Predicting Protein Structures

• Main Author: Khairudin , Nurul Bahiyah Ahmad
• Format: Thesis
• Language: English
• Published: 2009
• Subjects: RS1-441 Pharmacy and materia medica
• Online Access: http://eprints.usm.my/41798/1/Nurul_Bahiyah_Ahmad_Khairudin24.pdf; http://eprints.usm.my/41798/

Proteins are the building block of life. Knowledge of the three dimensional structure of proteins is of fundamental importance in understanding protein function. In this study, a new computational method was developed to predict these structures by combining the knowledge-based homology modeling and the physics-based molecular dynamics simulation methods. The core region of the protein wasinitially constructed via homology modeling based on sequence similarity with other solved protein templates. Then, the remaining end-terminal regions were allowed to fold towards the core region via MD simulation a few residues at a time. The method was categorized into three parts; the development of the core region of the protein, the development of the complete protein structure and the MD refinement simulation