Protein structure alignment with a dynamic programming algorithm using dihedral angles

• Main Author: Ang, Seok Yan
• Other Authors: Tan Ching Wai
• Format: Final Year Project
• Language: English
• Published: 2009
• Subjects: DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences
• Online Access: http://hdl.handle.net/10356/17012
• Institution: Nanyang Technological University

In molecular biology, a common question often rises about a gene or protein is whether it is related to any other gene or protein. One of the most widely used approaches to distinguish if they are related is by sequence alignment. However, research has shown that sequence alignment has its limitations, where aligned sequences indicating high similarity may not share similar properties and vice versa. In this project, a structural approach is adopted to improve the sequence alignment. The structural information of the protein is analyzed, based on the alignment of proteins dihedral angles through a dynamic programming algorithm. A short introduction on the bioinformatics field was given where various biology terms and databases were explained. Past research and findings were also discussed. Structural information from PDB files was translated into dihedral angles. Alignment techniques and distance functions were then applied in the algorithm with different cost models and the resulted alignments were benchmarked. A research on some existing structural alignment algorithm was also performed. The benchmarking tool used was the Shift Error Algorithm and the results were benchmarked against one of the known existing algorithms, Dali. Although the results were not promising as Dali, there were several recommendations that could be carried out for future enhancements, such as modifying the dynamic programming cost mode and comparing subset of residues instead of single residues.