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FeatureMap3D combines protein sequence-based information with structural data from the Protein Data Bank (PDB).

Each query sequence is aligned to the best hit in PDB. The hit is visualized by mapping the alignment onto the PDB structure using color-coding for match/mismatch gaps etc. User provided feature annotation (e.g. phophorylation sites, evolutionary interesting sites or pattern of alternative splicing) can also be mapped onto the PDB structure.

Instructions Output format Software download Article abstract

Input sequences

Paste in one or more protein sequences in FASTA (sequence only) or TAB (sequence and annotation) format into the field below:

Alternatively, upload a file containing the sequences ( FASTA or TAB format) directly from your local disk:

View example input sequences.

Descriptive sequence feature annotation can be addded in the field below:

Hit Submit to run the search with default parameters, or custimize the settings below
Expected running time: appx. 1 minute per sequence.

Search options

The following options governs the generation of the GetStruct data file. Visualization is constructed from this data. The raw GetStruct data file is especial useful for computational analysis and it can be downloaded from the result page

Customize search  Consider up to   BLAST hits in PDB per query sequence (only the best is shown)
Mask low complexity regions in the query sequences
Skip non-X-ray entries in PDB

Customize selection Show all hits (no selection, the criteria below will not apply)

 Discard all hits with sequence similarity to the query lower than  %
 Discard all hits to chains shorter than    amino acids
 Discard all hits with resolutions lower than Å
Discard all hits with no annotated sites

Customize output Include the selection details for each query sequence

Visualization options

The following options governs the visulazation of the GetStruct hits. The images are created using the PyMol software. Please notice that the generated PyMol script, along with the relevant PDB file, is available for download as a packed archive, making it very easy to refine the visualization on your own computer.

Color scheme

Black background
White background
Black background is the best for viewing the structure on the computer - white background is the best for printing.

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB
Rasmus Wernersson, Kristoffer Rapacki, Hans-Henrik Stærfeldt, Peter Wad Sackett, and Anne Mølgaard
Nucl. Acids Res. 2006 34: W84-W88

View the abstract.


The software suite behind the FeatureMap3D server is open source software (GPL license) and can be downloaded here.

If you require FeatureMap3D on a commerical license, please contact


Scientific problems:        Technical problems: