• To execute a single query, enter a single identifier (Uniprot, gene symbol, or Ensembl transcript) and all of its associated mutations.
• Mutations may be entered as numbers corresponding to the sequence location of the mutation, or in popular mutation formats.
• The mutation type should match the identifier type—nucleotide mutations should be provided when an Ensembl transcript is used as an identifier, and amino acid substitutions should be provided in all other cases.

• To execute a batch query, enter one identifier per line followed by all of its associated mutations on the same line.
• Mutations may be entered as numbers corresponding to the sequence location of the mutation, or in popular mutation formats.
• Enter genomic locations in the format chr22:26070464 or genomic mutations in the format of chr22:26070464A>T with one such identifier per line.

• Upload a text file with one identifier per line followed by all of its associated mutations on the same line.
• Mutations may be entered as numbers corresponding to the sequence location of the mutation, or in popular mutation formats.
• Enter genomic locations in format chr22:26070464 or genomic mutations in the format of chr22:26070464A>T with one such identifier per line.

• Click on a row in the table to select a publication from the COSMIC database to analyze.
• Use the Search field to find a publication of interest by entering any combination of last author name, tissue, year, journal, or PubMed ID.
• If you select a publication that investigates more than one tissue, please select the tissue you want to analyze in the box below the table.

• Select values to define what it means for amino acids to be in a cluster.
• Cluster Size is the number of mutations that must be in a cluster allowing for more than a single substitution per amino acid or the same substitution repeated more than once.
• Unique Amino Acids only count the number of unique numerical indices of amino acids in a cluster.
• Intracluster Distance is the diameter of the tightest sphere containing all amino acids in a cluster.

In addition to clustering mutations on all available PDB structures, mutation3D uses a selection of homology models from ModBase to increase its coverage of the proteome. These models are graded by their accuracy based on several criteria. These options are suggested for advanced users only.