Studying the Use of VINA and PLANTS in Protein-Peptide Docking

Date of Award


Degree Type


Degree Name

Master of Science (MS)



First Advisor

Prof. Joseph Audie


Summary: Two different computational protein-ligand docking programs, namely VINA and PLANTS, have been analyzed for their ability to predict the docking behavior of fifty three small peptides contained in the LEADS-PEP database. The comparison of the obtained VINA results enabled us to verify previously published results according to which both docking methods provided accurate results for the description of the docking behavior of small peptides. The PLANTS results extend previous work and reinforces the usefulness of small molecule docking programs for docking small peptides. However, both methods failed to provide an accurate model for the docking behavior of bigger peptides, as indicated by primarily increasing RMSD values with respect to control x-ray crystal structures. These results are comparable to those described in the literature, according to which the size of the peptide has a significant influence on the ability to model its binding behavior by using small docking methods like VINA and PLANTS.


Master's thesis presented to the Department of Chemistry, Sacred Heart University.