Given the amino acid sequence of a putative alpha-helical membrane protein, SCAMPI predicts the topology of the protein, i.e. a specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane. The prediction is based on an experimentally determined scale of free energy contributions from each amino acid to helix insertion efficiency. See the SCAMPI2 paper for a detailed description of the method. Note that the server does not predict cleavable signal peptides, which are easily confused with TM segments. If signal peptides are likely to be present in the input data, please use TOPCONS, which predict also the signal peptide.

This work used the EGI infrastructure with the support of IN2P3-IRES, INFN-CLOUD-BARI and TR-FC1-ULAKBIM.

This server is appropriate for topology predictions of large protein datasets. Input to the server is amino acid sequences in FASTA format. Using the text window, the maximum number of characters to be pasted is 100,000, or using the file upload option, the maximum number of sequences per query is 100,000 (i.e. enough for all bacterial and even most eukaryotic proteomes). If you only have one or a few sequences, use the TOPCONS server instead.

The server outputs prediction results in three text files:

• Predicted topologies: Text file containing the predicted topologies for all proteins in a FASTA-like format, where i=inside (cytoplasmic side), M=membrane and o=outside (extra-cytoplasmic side).
• List of predicted TM proteins: A list containing the names of all proteins with at least one predicted TM region.
• List of predicted non-TM proteins: A list containing the names of all proteins with no predicted TM regions.