The home page allows the user to input details of a variant and request analysis of this by Missense3D-TM. There are two main ways in which to specify the query variant:
Please select the button marked "Position on 3D Structure" to input a variant as a residue position on a 3-d structure file. 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).
Select the button marked "Position on Protein Sequence" to input a variant as a position within a Uniprot sequence. The Input requires the protein UniProt ID, amino acid position, substitution and the PDB ID of the experimental 3D structure. You cannot upload your own structure here.
To view the input panel for variant specification within a structure file click
Position within a structure file
If you choose to input your variant details as a residue identifier within a 3-d structure, the following input panel will be displayed to allow you to specify the details of the variant you wish to analyse.
Note: You should enter a PDB code if you wish to use a standard 3-d structure from the PDBe database. Alternatively, you should use the 'Browse' button to upload your own structure file which contains your variant. In either case, the residue position that you supply should match the residue identifier of the variant residue in your selected structure file.
To view the input panel for uniprot variant specification click
Position within a UniProt Sequence
If you choose to input your variant details as a position identifier within a uniprot sequence, the following input panel will be displayed to allow you to specify the details of the variant you wish to analyse.