Date of Graduation

Spring 2015

Document Type

Honors Research Project

Degree Name

Bachelor of Science


Chemical Engineering - Cooperative Education

Research Sponsor

Donald P Visco, Jr

First Reader

Nic D Leipzig

Second Reader

Jie Zheng


This Honors Project focused on a few aspects of this topic. The second is comparing the molecular signature kernels to three of the BLOSUM matrices (30, 62, and 90) to test the accuracy of the mathematical model. The kernel matrix was manipulated in order to improve the relationship by focusing on side groups and also by changing how the structure was represented in the matrix by increasing the initial height distance from the central atom (Height 1 and Height 2 included).

There were multiple design constraints for this project. The first was the comparison with the BLOSUM matrices (30, 62, and 90) which characterized the substitution ability of each pair of amino acids as found in nature. The last constraint was the usage of the signature kernel equation which was used in order to repeat a previous study by Jean-Loup Faulon.

The manipulated kernel matrix including side groups improved the linear correlation from 0.83 to 0.87. While using Height 2, the linear correlation R2 improved from 0.83 to 0.93. From the results, polarity is a factor for structure as in nature and using height 1 or a two-dimensional method will limit the results.