Missense3D | Structural Bioinformatics Group

Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures.

Please cite: Ittisoponpisan, S., Islam, S.A., Khanna, T., Alhuzimi, E., David, A. & Sternberg, M.J.E. (2019)
Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? J. Mol. Biol. 431, 2197-2212.
https://doi.org/10.1016/j.jmb.2019.04.009

Position Available with Professor Michael Sternberg
Job Opportunity for Experienced Bioinformatics Software Developer (Phyre and Missense3D) See:
https://www.jobs.ac.uk/job/CXG066/bioinformatics-software-developer-in-protein-structure-and-genetic-variant-modelling

Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures.

Choose your input from:

Position on Protein Sequence

The Input requires the protein UniProt ID, amino acid position, substitution and the PDB ID of the experimental 3D structure. A link to the available PDB structures is provided.
You cannot upload your own structure here.

or

Position on 3D Structure

This input page requires knowledge of the position of the residue of interest onto the 3D coordinate file (residue numbering in 3D structures does not always match the residue numbering of the primary amino acid sequence).
You can upload your own experimental or model structure (including AlphaFold models).

Variant information

UniProt ID

PDB code

OR upload here
(5MB limit)

PDB chain ID

Residue number

Residue ID

Wild-type amino acid (Required just as a check)

Please select a valid amino acid.

Mutant amino acid

Please select a valid amino acid.

Upload your PDB file(s)
(pdb, zip, or tar format)

Please provide variant information. One variant per line.

Example

#PDB #Chain #Residue No. #WildtypeAA #MutantAA
P06280 3hg3 B 52 Cys Arg
P00918 2fos A 107 His Tyr
*Each column is separated by a space.

Example

#PDB #Chain #Residue No. #WildtypeAA #MutantAA
3hg3 B 52 Cys Arg
2fos A 107 His Tyr
*Each column is separated by a space.

Email (under construction)

Or choose from examples (click to apply) 3hg3 (B) | 52 CYS > ARG 2fos (A) | 107 HIS > TYR 1x3s (A) | 24 LEU > GLN 1z70 (X) | 1348 ALA > PRO

Get your protein structure predicted

If the structure of the protein you wish to analyse is not available, you can get one using our in-house homology model predictor Phyre2.

Go to Phyre2 website

AlphaFold Models

You can now use AlphaFold models in Missense3D, just upload your AlphaFold model using the 'Position on 3D structure' mode. If you want to learn more about AlphaFold models please read our recent Perspective article in Journal of Molecular Biology available at https://doi.org/10.1016/j.jmb.2021.167336

Please see the Missense3D Licence, Disclaimer and Terms and Conditions of Use by clicking on this link.

Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures.

Please cite: Ittisoponpisan, S., Islam, S.A., Khanna, T., Alhuzimi, E., David, A. & Sternberg, M.J.E. (2019) Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? J. Mol. Biol. 431, 2197-2212. https://doi.org/10.1016/j.jmb.2019.04.009

Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures.

Choose your input from:

Position on Protein Sequence

or

Position on 3D Structure

Variant information

Get your protein structure predicted

AlphaFold Models

Please cite: Ittisoponpisan, S., Islam, S.A., Khanna, T., Alhuzimi, E., David, A. & Sternberg, M.J.E. (2019)
Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? J. Mol. Biol. 431, 2197-2212.
https://doi.org/10.1016/j.jmb.2019.04.009