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<meta name="description" content="Conserved Domain Database (CDD) models and 3D protein structures relevant to SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. This is a resource of the National Center of Biotechnology Information (NCBI), National Library of Medicine (NLM)">
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<meta name="keywords" content="proteins, functional, conserved domains, 3D structures, macromolecular structures, severe acute respiratory syndrome coronavirus 2, architecture, coronavirus, pandemic, SARS-CoV-2, COVID-19">
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<br>
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<title>How to search the Protein Family Model database</title>
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<style>
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<div class='largetitle'>How to search the Protein Family Model database</div><br>
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<div>
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The Protein Family Model database can be queried using a variety of terms, including any name known for the model, the full name or a substring of the name of a protein, a gene symbol, a publication, or the type of model (Sparcle or Conserved domain architecture, BlastRule, or HMM).
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</div><br>
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<div class='title'>Examples</div>
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<ul>
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<li>"IniC" returns protein family models where the term IniC appears in the model name, its description, gene symbol, or a publication title.
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<li>"iniC[GeneSymbol]" returns protein family models with the gene symbol iniC
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<li>"isoniazid[Description] AND blastrule[Method]" returns any BlastRule where the text describing the BlastRule contains the term "isoniazid".
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</ul>
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<div class='title'>Commonly used search terms</div><br>
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<table border='0' cellpadding='10' cellspacing='0'>
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<tr><th>Search term</th><th><span style="white-space:nowrap;">Applies to</a></th><th>Description</th><th>Example</th></tr>
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<tr><td>EC</td><td>All</td><td>Enzyme Commission number associated with the family model</td><td>"2 8 1 4 "[ECNumber]</td></tr>
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<tr><td>ECTitle</td><td>All</td><td>Enzyme Commission name or part of name associated with the family model</td><td> sulfurtransferase[ECTitle]</td></tr>
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<tr><td>FamilyAccession</td><td>All</td><td>NCBI Accession</td><td>nf003559[FamilyAccession]</td></tr>
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<tr><td>FamilyAccessionOrig</td><td>HMMs</td><td>Accession in source database (Pfam PF14200.6, PRK PRK05234)</td><td>prk05234[FamilyAccessionOrig]</td></tr>
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<tr><td>GeneDescription</td><td>Sparcle</td><td>Name or part of name of gene associated with the family model</td><td>sulfur[GeneDescription]</td></tr>
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<tr><td>GeneSymbol</td><td>All</td><td>Gene symbol associated with the family model</td><td>mgsA[GeneSymbol]</td></tr>
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<tr><td>Method</td><td>All</td><td>Family model type (blastrule, hmm, or sparcle)</td><td>sparcle[Method]</td></tr>
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<tr><td>ProductName</td><td>All</td><td>Name or part of a name associated with the family model</td><td>"methylglyoxal synthase"[ProductName]</td></tr>
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<tr><td>PubmedID</td><td>All</td><td>Pubmed publication ID associated with the family model</td><td>1704886[PubmedID]</td></tr>
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<tr><td>PublishDate</td><td>All</td><td> Family Model publication date or date range</td><td> ("2020/01/01"[PublicationDate] : "2020/02/01"[PublicationDate])</td></tr>
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<tr><td>ReviewLevel</td><td>Sparcle</td><td><a href="https://www.ncbi.nlm.nih.gov/Structure/sparcle/docs/sparcle_help.html#SummaryPageReviewLevel">Curated, autonamed, or named by domain</a></td><td> reviewed[ReviewLevel]</td></tr>
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</table>
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<br>
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<div class='title'>Search results</div><br>
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<div>
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The Search results include the following information for each model matching the search:
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<ul>
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<li>The model name, encapsulating the function of the proteins in the family represented by the model
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<li>A description of the function of proteins in the family or of the biological process in which proteins in the family are involved (if available).
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<li>The date on which the family model was published
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<li>The model accession number for the family
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<li>The type of model (HMM, BlastRule, or Sparcle)
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</ul>
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</div>
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<div class='title'>Individual records</div><br>
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<div>
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Clicking on a search result opens a page that is specific for the model that was selected.
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Information displayed in these records is different for HMM, BlastRules, and Conserved domain architectures. For more information, see the help documentation linked from the individual records.
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</div>
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<br>
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<div class='title'>Accessing the protein family models</div><br>
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<div>
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Protein family models are available for download:
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<ul>
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<li>HMM models: <a href="https://ftp.ncbi.nih.gov/hmm/current">https://ftp.ncbi.nih.gov/hmm/current</a>
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<li>BlastRules: <a href="https://ftp.ncbi.nih.gov/pub/blastrules/">https://ftp.ncbi.nih.gov/pub/blastrules/</a>
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<li>Conserved domain architectures: <a href="https://ftp.ncbi.nih.gov/pub/mmdb/cdd/">https://ftp.ncbi.nih.gov/pub/mmdb/cdd/</a>
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</ul>
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</div>
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</body>
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</html>
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<br>
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Revised 20 October 2020
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