iSuperpose: A comprehensive tool to superpose protein structures.

This tool will perform the 3D superposition of protein structures by best superimposing the alpha-carbons (or the backbone) of the proteins given a alignment specifying the correspondence between the structures. If no alignment is provided, a structural alignment will be calculated using TMalign. One the alignement is identified, the superposition is achieved using a quaternion based procedure using a specific eigen value calculation implementation. See QBestFit.

Unlike most superposition tools, iSuperpose can iteratively perform the iterative superposition of several files onto a reference, or all the crossed superpositions of two series of files. You can specify 1 or 2 files. Each of them can correspond to multi-PDB files, or multi-model PDB files. A multi-PDB file is one file consisting of PDB files piled up, delimited by HEADER / END lines (mandatory). A tool to pile up PDBs is here . Alternatively, you can also paste into the text area PDBIds, or even the url of a remote multi-PDB file, or a remote list of Ids. Ids are on the form: 1tim (whole PDB 1tim entry) or 1timA (chain A of the 1tim entry).

If you specify only one file, all the PDBs or all the models (using the MODEL / ENDMDL terminology) contained in the file will be superposed onto one specified model or PDB, corresponding to the "reference rank" (default is rank 0, i.e. the first entry).

When specifying only one PDB file, you can specify the alignment used to superpose the proteins, by providing a FASTA format alignment.If a multiple file is input, you can specify a multiple alignment. For each protein, uppercase residues are considered to perform the superposition, lowercase residues are not involved in the superposition. The order of the sequences of the alignment must match the order of the PDB files in the multi-PDB data.

If you specify two files, all the PDBs of file 1 will be superposed on all the PDBs of file 2. PDBs of file1 are fixed. PDBs of file2 are moving (superposed).

Note that:

• PDB files MUST currently have not more than one chain.
• Non standard amino acids are not accepted.