Input data can be PDB/Uniprot accession number (e.g. 1ASY/P04802), gene name (e.g. DPS1), or other keywords (e.g. aspartyl-tRNA synthetase), and click Enter or Search to view the results. Please refer to Figure 1.
Figure 1. Query the database.
The server will return the result of the fuzzy query (Figure 2). Fuzzy matching information includes PDB ID, protein names, Uniprot IDs, gene names and organism. Users can select one complex to view the mutagenesis data.
Figure 2. Query results.
The Browse page (Figure 3) shows the mutagenesis experiment information of each residue including temp, Kd, ΔG, ΔΔG and reference. Users can view all the mutations or mutations in protein-DNA complexes or mutations in protein-RNA complexes.
Figure 3. Browse the mutagenesis data.
The binding free energy of wild type and mutant for a complex is shown in Figure 4.
Figure 4. Detailed mutagenesis information of a complex.
Figure 5 shows the detailed protein information including Uniprot ID, Protein names, Organism, Gene names, Binding site, Gene ontology IDs, PubMed ID, InterPro domain, Interactions (STRING) and eggNOG..
Figure 5. Protein information.
Users can view the protein complex and its mutagenesis data in 3D model (Figure 5).
Figure 6. 3D view of the protein.
The ΔΔG scores for each residue are listed at the bottom. Interactive operations are also provided (Figure 5).
Figure 7. Interactive operation.
The Nabe API allows you to access mutagenesis data in a programatic fashion. The Nabe API can be used with simple HTTP requests from any tool or programming language of your choice.
This api allows you to retrieve filtered lists of mutants in json format. Filter parameters can be added to the query string of the request to filter the returned list.
| Parameter | Description | Example |
| pdb | This parameter should be a PDB code you would like to see mutants for | pdb=1ASY |
| keyword | This parameter can be PDB/Uniprot accession number (e.g. 1ASY/P04802), gene name (e.g. DPS1), or other keywords (e.g. aspartyl-tRNA synthetase) | keyword=tRNA |
Returns all mutants of DPS1 (PDB:1ASY).
[{
"Mutant": "WT",
"Temp": "310",
"Kd": "3.00E-08",
"DelG": "-10.632",
"DelDelG": "-",
"PubmedID": "10452887",
"Chain": "A"}
{ "Mutant": "D 210A",
"Temp": "310",
"Kd": "3.28e-07",
"DelG": "-9.164",
"DelDelG": "1.468",
"PubmedID": "10452887",
"Chain": "A"}
...}]