Protein-Peptide Docking: Construction of a Protein-Peptide Database and Docking the Peptides into Target Proteins

Date of Award


Degree Type


Degree Name

Master of Science (MS)



First Advisor

Joseph Audie, Ph.D.


The purpose of this paper is to study the application of small molecule docking algorithms to the problem of protein-peptide docking. Protein-peptide docking is significant because it can be used to aid in the development of peptide-based drugs, which can provide safe and effective ways to treat many diseases. The present study aims at strengthening and extending our knowledge about the small molecule docking algorithms. When it comes to docking peptides, is clearly important and of significant interest. In the present study, particular attention is given to systematically docking 53 peptides from the Leads-Peb database using the small molecule docking programs, Vina, and Plants an implemented in the Vega ZZ molecular modeling software environment. Results were analyzed using standard analytical and statistical methods and appropriate conclusions were drawn. The main conclusions of the study are that Vina and Plants can be used to successfully dock small peptides, with Vina slightly outperforming Plants. However, neither program succeeds at docking peptides larger than about seven residues. As such, new docking methods are required for docking larger peptides. It is hoped that this paper will be useful to researchers when it comes to researchers making smart choices for docking peptides into protein targets.


Master's thesis submitted to the faculty of Sacred Heart University's Chemistry Program in partial fulfillment of the requirements for the degree of Master of Chemistry.