Welcome to Home Page of PPDbench

Introduction:This server is made in order to provide an easy webserver to calculate FNAT, L-RMSD and I-RMSD values of docked and original poses of protein-peptide complexe's. User's can calculate these values either for a single docked complex using 'Single module' or for multiple complexes using 'Batch module'. We also provided the dataset of 133 complexes on which we performed our benchmarking study of five widely used docking softwares, ATTRACT, Hex, ZDOCK, PatchDock and pepATTRACT. User's can take help from Help page if they face any problem while using the server

  • Single docking pose evaluation: This module allow users to evaluate the performance of a docking pose corresponding to any peptide-ligand complex used in this study.
  • Benchmarking of a docking software : User may evaluate their docking software on 133 protein-peptide complexes used in this study. This is useful for understanding quality of newly developed docking software.
  • Compare two docking poses: This module is developed for comparing two docking pose or quality of docking if user provides original and docked pose.
    Reference: Agrawal et al., (2019) Benchmarking of different molecular docking methods for protein-peptide docking. BMC Bioinformatics201919 (Suppl 13) :426