Search

Search help

Integrated search

This search service allows you to more quickly find biomolecular and biochemical information resources archived by BMRB, PDB, EMDB, Swiss-Prot, BMRB-Metabolomics and Ligand Expo. Though the results are shown in entry lists by each information resource, each entries have mutual references if either entity or sequence matches. The results also annotated by other information resources such as PubMed, IntAct and PubChem.

Please select tabs titled with either "Everything" or "Sequence" for keyword search or BLAST sequence search, respectively.

Omni-box

The omni-box allows you to find effective keywords or sequences while you're typing.

omni-box

Filters

When you click a button located left side of the omni-box, search filter appears to set filtering results by release date, author names, polymers, ligands and source organisms of entity. Auto-suggestion functionality is also implemented like the omni-box.

search filters

Settings

A "cog" button on the omni-box allows you to change various search settings; target databases, hits per page, query settings, BLAST settings and miscellaneous display settings. Some changes will take effect after "OK" button is selected.
Please select "Close" button to hide this panel without changes.

search settings

Query syntax

The search service supports Lucene-style query syntax for composing a complex query. The input fields for the search filters also support the query syntax. A query is broken up into single term, phrases (a group of terms surrounded by double quotes) and operators. Multiple terms and phrases separated by a white space are automatically conjugated by "AND" operator, but you can change the default operator in the search settings panel.
The query syntax allows you to use the phrase, wild card (either ? or * character in term), regular expression surrounded by slashes, fuzzy search based on Demerau-Levenshtein distance using a tilde character in term end, proximity search (e.g. "ph domain"~3, which searches for "ph" and "domain" within 3 words.), range search for decimal or date attributes (e.g. entry.original_release_date:[20010101 TO 20051231]), a series of Boolean operators ("OR", "AND" and "NOT") and grouping using parentheses to form sub queries that is useful if you want to control Boolean logic for a query. Please refer to the link above.


Result panel

The entry lists are grouped by each database, such as BMRB, PDB, EMDB, Swiss-Prot, BMRB-Metabolomics and Ligand Expo. "Order by" menu button allows you to sort by various conditions, such as relevance, release data, accession ID, experimental method, citation counts citation title, total formula weight, maximum entity weight, related entries, etc. Linked words can be used for next search using the selected keyword. Various linked apparatuses are key buttons to show more detailed results interactively.

Statistics of obtained results are available under the results panel. A green button next to pagination buttons is a short cut button to the statistics.

search results

Statistics panel

The statistics are shown as charts as below. The charts summarize the following points. Released entries, Total molecular weights, Available data sets (BMRB), Completeness of assigned chemical shifts, Highest resolution (PDB, EMDB), R-value (PDB), Applied experimental methods, Applied refinement methods, Cited journal names, Most frequent keywords and Most frequent entry author names, respectively.

search results

What's new?

nmrML documents are accessible from metabolomics entry page.

BMRB/JSON archive is accessible from entry page.

Chart representations about Spectral density values and D-CSA cross correlation relaxation rate are available.

Table representation about pH titration is available. Fitted pH titration curve will be displayed, if possible.

Table representation about Binding constants and Chemical rates are available.

Chart representations about Coupling constants and RDCs are available.

Chart representations about Hydrogen exchange protection factors and Hydrogen exchange rates are available.

Chart representation about Order parameters is available.

Chart representation about T1/T2 with band plots stand for NOE value lower than 0.5 is available.

Chart representations about Heteronuclear T1, Heteronuclear T2 relaxation, Heteronuclear T relaxation and Heteronuclear NOEs are available.

Release date is added in "Entries sharing articles" content.

Deposition code can be used for searching BMRB entry page.

Chart representation about completeness of assigned chemical shifts is available. Assigned chemical shift table for Metabolomics entries are also available.

Fraction of assigned chemical shifts per residues is available under table about completeness of assigned chemical shifts. In addition, you can download assigned chemical shifts in various formats and access sample information.

Experiment information is available as "Experiment performed" context for BMRB and Metabolomics entries. Spectral images for metabolomics entries are also available.

Entry view page is available for Metabolomics entries. e.g. Metabolomics bmse000400 entry

Sorting in reverse order has been implemented and accessible next to "Order by" menu.

Query history has been implemented and accessible from a clock icon on Search panel.

Entry view page is available for BMRB entries. e.g. BMRB 15400 entry

Fully implemented top search v3's functionality.

  • Hit contexts with highlight
  • Statistics panel
  • Exporting search results by CSV, TSV, XML and JSON formats