Overview
The MTR3D-AF2 website provides an easy-to-use interface allowing users to visualise and download MTR scores calculated utilising spatial information derived form AlphaFold2 structures, enabling identification of regions under purifying selection. MTR scores calculated using sequence based information are also available.
Supported browsers: Chrome, Firefox, Opera and Brave.
Interpretation
The Missense Tolerance Ratio (MTR) aims to quantify the purifying selective pressure acting upon residues in the proteome. MTR3D-AF2 allows users to explore these through a 2D sequence-based representation and a 3D structure based representation. An MTR score is derived by comparing the observed proportion of missense variation obtained from gnomAD and UK Biobank to a dataset of variation generated to simulate an absence of selective pressure. Regions with a score of 1 can be interpreted as being under neutral selective pressure, whereas those with scores less than 1 can be interpreted as having some degree of intolerance to missense variants due to purifying selective pressure acting upon them.
Searching for a Protein of Interest
MTR3D-AF2 enables users to search for their protein of interest using a uniprot id, uniprot accession code or a GENCODE transcript. However, as the MTR3D-AF2 scores have only been calculated on the canonical version (UP000005640) of each protein, only those transcripts which match the exact residue sequence of the canonical version of the given protein are available.
After clicking on the browse section on the home page, the page below will be displayed. The results of the browsing mode or a specific search are shown as an interactive table as depicted in the image below. In this case, a user provided the term "MC4R" (1), which was matched with a single entry. If no entry is matched after searching for the common name of your protein of interest, search for the uniprot accession of that protein instead as the Uniprot_ID does not always align with the protein's common name. The number displayed in the confidence column (2) is the mean pLDDT score (structure confidence score). By clicking in the "Details" button (3) for a particular record, users will be redirected to the data visualisation page.
Using the MTR3D-AF2 Viewer
The "Details" page for a particular entry is divided into three sections: controls and sequence-based representation, structure-based viewer and a downloads section.
Sequence-Based Representation
The sequence-based representation section presents identifiers of the sequences (UniProt ID and accession code) (1). Users have the options to choose which scoring version to show, either MTR3D-AF2 or the sequenced based MTR version MTRv2, as well as select different window sizes (2). The 2D MTR distribution for a gene is plotted across the protein-coding sequence (x-axis showing Amino-Acid Position). Users have the ability to zoom, pan and save the plot using right-hand control panel (3). Users have also the option to highlight specific residues of interest (4), which will also be shown in the structure-based representation.
Structure-Based Representation
Users are able to visualise MTR scores on the AlphFold model, representing the scores using a colour scale where red represents intollerance and blue tolerance (1). Users are also able to change the colour scheme using a drop down button (2) in order to see many other scores mapped to the structure including the pLDDT scores representing AlphFold2's confidence in their prediction of that particular region of the structure.
Downloading MTR Data
Finally, users have the option to download the information presented within the “Details” page, including MTR3D-AF2 and MTRv2 calculations as well as the protein structures shown.
