Users can upload the genome variations of their interest by pasting them in a search box or uploading a file containing them. A Variant Call Format (VCF)-like input is expected, i.e. the first to the fifth columns indicate chromosome, position, SNP ID, reference allele and alternative allele, respectively, but the first two columns (chromosome and position) are mandatory. Before submitting, users can select options to filter variations with conformational annotations to focus on those that they consider are worth examining in detail with respect to the effects on protein functions.

Searching structures for genomic variants from the main page

Enter genome coordinates in the text box or upload a file that contains the genome coordinates. Users can focus on the variants that are mapped to the structures passing several filters by using following “Search options”.

Result Summary page

In the result summary page, among the variations searched in the main page, those variations that are mapped to at least one PDB structures that satisfy the specified search options are listed in a table. Each row of the table corresponds to a variation in the input.

Base and amino acid change column shows the changes in mRNA and amino acid sequences in the RefSeq database, together with the description of the mRNA. The summary column shows the summary of the structural features of the mapped amino acids. As a single variant can be mapped to multiple amino acids from different PDB files, numerical structural features are summarized in the form of “median (min-max)(number)” if multiple values exist or “value (number)” if all of the vales are the same, whereas categorical features such as disorder and secondary structures are summarized by the fraction of each feature value.

Each column of the summary information indicates The detail column shows links to the pages for the annotated variations.

Variant Page

A variant page displays the structural features of all of the mapped amino acids in the PDB for a given variant and can be accessed by clicking the “detail” column in the result summary page.

The table on the top of the page shows variant information including chromosome, position, ID, reference and alternative alleles, base and amino acid changes and the description of mRNA.

Below the variant information table is a MolMil structure browser, which highlights the mapped amino acid and the subunit in which the mapped amino acid is included.

In the bottom, all of the mapped amino acids are shown in a table format. The columns are roughly divided into entity, residue, monomeric, bio-unit, ligand and view.

The entity columns describe the mapped protein in the PDB and sequence identity between the human protein and the mapped protein The residue columns describe the identities of the mapped residues “label” and “auth” indicates annotations provided by PDB staff and by the authors, respectively. “asym_id” specifies one of the subunits in a PDB entry and “seq_id” indicates the residue number in the subunit. “Name” is taken from “label_comp_id” record in mmCIF files.

The monomeric columns describe the structural features of the mapped amono acids in a monomeric state of the protein, i.e. the coordinates of the protein subunit is virtually isolated from the other coordinates in the PDB file. The biounit columns describe the structural features of the mapped amino acids in a biological unit, a biologically active protein conformation. The ligand columns describe the interactions between no-protein residues and the mapped amino acids. The view column shows a “view” button. By clicking the button, you will see the structure of the mapped amono acid in the MolMil window.