PPDbench allows user to calculate CAPRI based evaluation parameters (FNAT, L-RMSD and I-RMSD values) between original and predicted protein-peptide complexes. This webserver consist of three modules.

SINGLE, this module allows user to calculate FNAT, L-RMSD and I-RMSD values for a single complex. In this module users need to upload one original and one predicted protein-peptide complex in PDB file format.

Important Instructions to be followed while using Single module of PPDbench

1. Only PDB file format is acceptable. No other file format is accepted.

2. Original as well as predicted protein-peptide complex should contain only single chain of receptor and single chain of peptide. File having more than one chain of receptor or peptide will not give results.

3. By default result page will display all three i.e. FNAT, L-RMSD and I-RMSD values.

4. For user's ease we provided examples file of original as well as predicted pose. User can download the example files by clicking on the Example tab.

BATCH Using this module users can calculate these values for a set of complexes. User can upload a zip file for diffrent poses of a protein-peptide complex or various poses of many protein-peptide complexes.

Important Instructions to be followed while using Batch module of PPDbench

1. Only PDB file format is acceptable. No other file format is accepted.

2. Original as well as predicted protein-peptide complex should contain only single chain of receptor and single chain of peptide. File having more than one chain of receptor or peptide will not give results.

3. User need to submit the original pose and its corresponding predicted poses in a single zip file named work.zip. Zip file other than this name will not give result

4. User can submit maximum number of 20 predicted poses for a single original pose. More than 20 predicted pose will not give proper result as server takes only 20 poses into account.

5. User can submit as many number of PDB files in zip file but size of zip file should not exceed more than 1.5 MB.

6. User need to name their pdb files by the following name. Original file should be named as PDBID_o.pdb for e.g. 1cka_o.pdb and Predicted poses should be named as PDBID_p_1.pdb, PDBID_p_2.pdb for e.g. 1cka_p_1.pdb, 1cka_p_2.pdb and so on till PDBID_predicted20.pdb. The first four letters of file name of origial and predicted complexes should be same.

7. In the batch mode we provided service for user to get the result of whichever option is required. User can get the desired result by clicking on FNAT, L-RMSD or I-RMSD button.

8. For user's ease we have provided examples file. User can download the example files by clicking on the Example tab. This file gives an example of the required file. The name of all the pdb files should be according to the names given in the example files.

User can download Datasets that we used for the benchmarking study. All the original complexes, receptors and ligands are available in the datasets section for download.