Performance evaluation of flexible-receptor docking tools based on the peptide length

Molecular docking tools play pivotal roles as a critical method in the drug design process inrecent years [۱]. There are various tools that estimate how ligands and receptors bind and how strongtheir affinity is [۲]. Considering the widespread use of these tools, it is highly important to find outwhether their results are accurate or not [۳]. Moreover, taking into account the flexibility of receptorsand ligands, imposes significant complexity on the docking calculations [۴]. Peptides are among themost flexible ligands and have many applications e.g., as anticancer and antioxidant [۵]. This studyexamines how the length of peptides with ۳ to ۸ amino acids affects the performance of three tools thataccount for flexibility, i.e., ADFR software, and HADDOCK and MedusaDock servers. The ۱۹۰protein-peptide complexes used for this purpose were carefully extracted from the PROPEDIA databaseand were subjected to necessary processing. After performing the focused-docking, the sampling powerwas evaluated by the lRMSD parameter and afterwards, the results were analyzed. The findings indicatethat the average lRMSD declinations for each amino acid addition are ۰.۱۸, ۰.۷۱ and ۰.۸۲ Å forHADDOCK, MedusaDock and ADFR tools, respectively. Furthermore, the average success ratedeclinations including all distance cut-offs, for HADDOCK, MedusaDock and ADFR are ۰.۸۵%, ۳.۲۹%and ۳.۸۲%, respectively. This information demonstrates the superior and distinct performance of theHADDOCK over the other two tools. It seems that the peptide-specific calculations, similar to what wesee in the algorithm of the HADDOCK, are essential for producing reliable results. This study providesinsights for the selection and improvement of flexible docking tools for peptide-based drug design.

کلیدواژه ها:

Molecular docking ، Flexible receptor ، Peptide ، Sampling power ، lRMSD