SuperPose molecules image

SuperPose Version 1.0

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SuperPose is a protein superposition server. SuperPose calculates protein superpositions using a modified quaternion approach. From a superposition of two or more structures, SuperPose generates sequence alignments, structure alignments, PDB coordinates, RMSD statistics, Difference Distance Plots, and interactive images of the superimposed structures.  The SuperPose web server supports the submission of either PDB-formatted files or PDB accession numbers. 

Please cite the following: Rajarshi Maiti, Gary H. Van Domselaar, Haiyan Zhang, and David S. Wishart "SuperPose: a simple server for sophisticated structural superposition" Nucleic Acids Res. 2004 July 1; 32 (Web Server issue): W590W594. Click here for PDF.

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If your PDB file contains multiple copies of a structure(ie. NMR files) you only need to enter one file or accession number. For additional information on how to run SuperPose, click
PDB Entry A
Select the first PDB file
OR Enter a PDB accession number
PDB Entry B (Optional)
Select the 2nd PDB file
OR Enter a PDB accession number

Note: the uploaded file(s) must be in PDB format in order for this form to work.
Superimposing more than 2 files? Click here

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Output Options:
Output Image
Display the superimposed structures as:
Display the superimposed structures in:
Display the superimposed structures in:
Image Background Colour:
Alignment Options:
SuperPose can manage the sequence and structure alignments (default), or you can specify which residues you wish to align by filling in the following text boxes (doing so will override all other automated alignments and alignment options). Specify comma-separated ranges of residues in ascending order (eg. 5-14, 35-100, 115-140). Ensure the total number of residues in each textbox are equal (if superposing structures from 2 different PDB entries). For automated alignments, simply leave these boxes blank.
PDB Entry A: Restrict superposition to residues:  
PDB Entry B: Restrict superposition to residues:  
Advanced Options:
Secondary Structure Alignment:
Guide the superposition with a secondary structure alignment rather than a sequence alignment when pairwise sequence identities fall below: %.
Subdomain Matching:
SuperPose can look for structurally similar and dissimilar regions between aligned protein chains. This is useful in identifying hinge motions, mobile segments, etc. If SuperPose finds structurally dissimilar regions, it will superpose the structures based on the single longest structurally similar region shared by the sequences.
Subdomain matching:
Minimum Sequence Similarity:
Look for subdomain matches and mismatches (e.g. hinge regions) for sequences with pairwise sequence identities above %.
Similarity Cutoff:
Identify as 'similar' aligned alpha-carbon atoms with RMSDs less than Angstroms.
Dissimilarity Cutoff:
Identify as 'dissimilar' aligned alpha-carbon atoms with RMSDs greater than Angstroms.
Dissimilar Subdomain:
The minimum number of contiguous alpha-carbon atoms with RMSDs above the Dissimilarity Cutoff (above) required to be considered a 'dissimilar' subdomain is residues.

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Questions or comments? Please use our feedback page!

SuperPose uses VADAR, BioPerl, WebMol, EMBOSS, ClustalW, MolScript, ImageMagick, and Gnuplot.

SuperPose v1.0 (2004) Rajarshi Maiti, Gary Van Domselaar, Haiyan Zhang, and David Wishart

Funding for this project was provided by    and