The New Jersey Institute of Technology's
Electronic Theses & Dissertations Project

Title:	A method for developing in-silico protein homologs
Author:	McClatchy, Susan
View Online:	njit-etd2003-009 (ix, 46 pages ~ 2.9 MB pdf)
Department:	Federated Biological Sciences Department of NJIT and Rutgers-Newark
Degree:	Master of Science
Program:	Computational Biology
Document Type:	Thesis
Advisory Committee:	Recce, Michael (Committee chair) Cohen, Barry (Committee member) Elbrecht, Alex (Committee member)
Date:	2003-01
Keywords:	Human genome Drug receptor candidates In-silico proteins
Availability:	Unrestricted
Abstract:	Computational methods for identifying and screening the most promising drug receptor candidates in the human genome are of great interest to drug discovery researchers. Successful methods will accurately identify and narrow the field of potential drug receptor candidates. This study details one such method. The method described here begins with the assumption that novel drug receptors have high sequence similarity to established drug receptors. The similarity search program FASTA3 aligns translated sequences of the human genome to known drug receptor sequences and ranks these alignments by measuring their statistical significance. Query results returned by FASTA3 are assembled into "in-silico proteins" or artificially generated homologs of known drug receptors. A second similarity search program, BLASTP, aligns in-silico proteins with a protein database, and also ranks alignments based on statistical significance. A potentially valuable in-silico protein identifies its generating drug receptor as the top-ranking result returned from the BLASTP search, and may represent a new family member of a particular group of drug receptors.