Implementing explicit solvent model of molecular dynamics simulation into protein rigid docking

• Main Author: Ng, Xue Ling
• Other Authors: Kwoh Chee Keong
• Format: Final Year Project
• Language: English
• Published: 2014
• Subjects: DRNTU::Engineering::Computer science and engineering::Software::Software engineering; DRNTU::Engineering
• Online Access: http://hdl.handle.net/10356/59991
• Institution: Nanyang Technological University

The development of scoring functions is important to protein-protein docking and in this project case, by running both ZDOCK and ZRANK will gives us a more accurate prediction of the docked positions. By using the benchmark 4.0 to run through ZDOCK, it gives us an initial ranking but there is still a possibility of much better docked positions in the list further down. By introducing ZRANK after finishing ZDOCK process, the prediction results are much more accurate. In this project, ZDOCK and ZRANK are used together with PyMoL and HBPlus in order to get the accurate results of the docking process.