Computational Characterisation of Protein-Protein Interactions

FAQ and Help

Input data

CCharPPI server uses three different sources of input data:

User custom PBD structures. This option is identified by the label 'Upload PDB structures'. When this option is selected, the user is asked to upload two separate PDB files, receptor and ligand structures respectively.
RCSB code. This option is identified by the label 'Select PDB by RCSB code'. When the user selects this option, CCharPPI polls the RCSB Protein Data Bank and download the PDB structure automatically (only if exists).
Compressed job file. This is the option for uploading large amount of data structures to be calculated by the CCharPPI server. Two different compression formats are accepted for this file: .tgz and .zip. The compressed job files has to contain a job.csv file and a set of different PDB files, two per complex (one for receptor and one for ligand). For each complex to be calculated, one line of the format 'pdb_file_1.pdb:A,B:pdb_file_2.pdb:A,C' is included in the job.csv file, where pdb_file_1.pdb is the PDB structure file for the complex receptor, pdb_file_2.pdb for the complex ligand and A,B are the chains to be used from the receptor PDB file and A,C the chains to be used from the ligand PDB file.

Note that the .tgz or .zip must contain only the job.csv and the PDBs files. If the files are stored within a directory, the server will report a malformed compress file. In other words, the files should be directly compressed without any folder.
```
tar my_data.tgz job.csv *.pdb
```
job.csv file example:
```
2OOB_rec.pdb:A:2OOB_lig.pdb:B
2UUY_rec.pdb:A:2UUY_lig.pdb:B
1HIA_rec.pdb:A,B:1HIA_lig.pdb:C
        
```
Download a working compressed job file as a example.

PDB structure files

CCharPPI server uses external tools in order to calculate the different descriptors. In order to avoid NaN invalid results for a given descriptor, be encourage to follow the PDB file format. Note that incomplete backbone or side-chain atoms may incur in inaccurate results and/or software failure.

Academic email address

This server is free to use for academics. The email address is used to confirm the affiliation. If you have an academic email but it is not accepted by our validation system, please, contact us.

Available descriptors

You can find the complete list of the available descriptors in CCharPPI server here: descriptors list.

Pre-calculated data

We have calculated the complete list of implemented descriptors in CCharPPI for SKEMPI, Bioinformatics (2012) 28(29):2600-2607, and Protein-Protein interaction affinity, Protein Sci. Mar 2011; 20(3):482-491 , databases:

Reference

To cite CCharPPI, please reference “CCharPPI web server: Computational Characterisation of Protein-Protein Interactions, IH Moal, B Jiménez-García and J Fernández-Recio, Bioinformatics 2014" (10.1093/bioinformatics/btu594). Authors should also cite the primary references of the methods that they use in their published works.