The iLoops Server uses protein structural features (protein loops as classified in ArchDB and/or domains as classified in SCOP) to determine whether any pair of proteins interact or not. To do that, it uses data from both known protein interactions and putative non-interacting proteins (co-localized, non-redundant, non-interacting random protein pairs non-similar to PPIs), assigning positive and negative scores to the structural features.

The main result page displays a summary of the predictions for the given protein pairs with available detailed data for each prediction. It also allows the download of all the predictions as a compressed XML file.

A detailed explanation on how to execute the server and interpret the results is found in Help:Server usage section. More information about iLoops can be found in Help:About iLoops section, Help:FAQ section and on: Planas-Iglesias, J. et al. Understanding protein-protein interactions using local structural features, Journal of Molecular Biology (2013).

The iLoops Server is limited to 25 protein pairs. If you want to analyze more protein pairs, please contact us: sbi+iLoops 'at' upf 'dot' edu.

iLoops: a protein-protein interaction prediction server based on structural features
Joan Planas-Iglesias; Manuel A. Marin-Lopez; Jaume Bonet; Javier Garcia-Garcia; Baldo Oliva
Bioinformatics 2013; doi: 10.1093/bioinformatics/btt401

  • First input box (SEQUENCES BOX): sequences of the protein pairs to be tested, in FASTA format. The first word in the FASTA header (between “>” sign and the first whitespace) will be used as identifier code for the protein.
  • Second input box (INTERACTIONS BOX): the protein pairs to be tested, indicated by the protein identifiers used in the previous box and separated by a double colon “::”.
IMPORTANT: Due to the importance of using the specific sequence provided by the user, the iLoops server only processes identifiers given in the SEQUENCES BOX. Hence, it does not retrieve sequences from external databases.

Sequences and Interactions


Sequences must be in fasta format. If the protein headers contains spaces, only the first segment will be considered.
Each interaction to test must be in a different row. The protein IDs, which must match with the fasta header, must be separated by double colon.

Parameters and Options