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Entrez Structure and 3D-Domains Index OverviewThe underlying database to support Entrez structure and 3D domains indexing is MMDB database. MMDB (a Molecular Modeling Database) is Entrez's macromolecular 3D Structure database. It contains experimentally determined biopolymer structures obtained from the Protein Data Bank (PDB). Entrez leads to vast information on biological function and molecular evolution by providing a number of powerful search tools useful for identifying structures of interest.Entrez's Structure Index page is the "home page" for querying 3D structures. For each query, it lists the PDB names and the general descriptions of the structures returned in the query result set. It also provides a number of links leading to further information. On the right hand side of the structure index page, for each returned structure entry, there is an "MMDB" button linking to the MMDB Structure Summary page, and a "Links" menu linking to Entrez 3D Domains Index, to Entrez Protein or Nucleotide Index, to Entrez PubMed Citations Index, or to Entrez Taxonomy Index, etc., where appropriate/applicable. Entrez's 3D-Domains Index page is the "home page" for querying 3D domains. For each query, it lists the domain names and the general descriptions of the corresponding structures of the 3D domains returned in the query result set. It also provides a number of links leading to further information. On the right hand side of the 3D domains index page, for each returned 3D domain entry, there is an "MMDB" button linking to the MMDB Structure Summary page, a "VAST" button linking to the VAST 3D-Domain Neighbors Summary page, and a "Links" menu linking to Entrez Structure Index, to Entrez Protein or Nucleotide Index, to Entrez PubMed Citations Index, or to Entrez Taxonomy Index, etc., where appropriate/applicable.
How To Make a QueryGo to the entrez page: http://www.ncbi.nlm.nih.gov/entrezFor Structure or 3D-Domains queries, choose the "Search Structure" or "Search 3D Domains" menu item at the top left of the page. There are four types of queries: (1) string query, (2) integer query, (3) date query, and (4) range query. For all these queries, write down in the text box the token to be queried followed by a field alias in square brackets. All queries are case-insensitive. By default, a string query without a field alias means query against [ALL]; an integer query without a field alias means query against [UID]. Date queries must have the following formats: YYYY/MM/DD, YYYY/MM/D (single digit month and day are allowed and don't have to be pre-padded by 0), YYYY/M/D, YYYY/MM, or YYYY, etc. Range queries are constructed by two tokens (a from and a to) separated by a : (colon) to specify the range, followed by a field alias in square brackets. All dates and all 'counts' (like resiude counts, helix counts, etc.) fields can be range queried. Apart from that, there are two additional fields that can be range queried: Resolution [RESO] in Structure Index and MolWeight [MWT] in 3D-Domains Index.
Range queries on Resolutions [RESO] (in angstroms) must have the following format:
Range queries on MoleculeWeights [MWT] (in daltons) must have the following format:
Range queries on Dates has similar format:
Range queries on 'counts' has format: Special Notes on Querying PdbChainCode [CHN]: PDB chain code can be a wide variety of characters including white-spaces (which can not be queried in Entrez). Also, PDB chain code is case-sensitive, whereas Entrez search engine is case-insensitive. In order to facilitate queries on special characters such as white-spaces, PdbChainCode queries can be done by inputting either the character itself or its corresponding decimal ASCII code. For example, in order to query PDB chain code 'A', you can input either 'A [CHN]' (which is interpreted by Entrez search engine to mean either 'a' or 'A') or '65 [CHN]' (to mean unambiguously the upper-case 'A' only); on the other hand, to query a white-space PDB chain code, you have only one choice: to input '32 [CHN]' (see examples below). In order to avoid upper/lower case ambiguity, it's recommended that you input PdbChainCode queries with decimal ASCII code. The following sections on Structure Query Capabilities and on 3D-Domains Query Capabilities list all the field aliases for different fields. One field may have several aliases, in which case, use the one you find most easily memorizable.
Query ExamplesFor queries on Entrez Structure:
tyrosine kinase For queries on Entrez 3D-Domains:
1b3oa1 [NAME]
Structure Query Result EntriesThe structure result entries include the following:
Structure Query CapabilitiesThe following fields can be queried in entrez structure index (with field aliases in square brackets; pick one alias that's easily memorized in case multiple aliases are available):
What are "3D-Domains"?3D-Domains within individual polypeptide chains in MMDB are identified automatically, using an algorithm that searches for one or more breakpoints, falling between major secondary structure elements, such that the ratio of intra- to inter-domain contacts falls above a set threshold. The 3D-Domains identified in this way provide means to increase the sensitivity of structure neighbor calculations, and to present 3D superpositions based on compact domains as well as on complete polypeptide chains. They are not intended to represent domains identified by comparative sequence and structure analysis, as modules that recur in related proteins, though there is often good agreement between domain boundaries identified by these methods. The structure similarities among individual chains and their compact 3D-Domains in MMDB are calculated by VAST algorithm, which superposes structures based on the structure alignments of their secondary structure elements.
3D-Domains Query Result EntriesThe 3D-domains result entries include the following:
3D-Domains Query CapabilitiesThe following fields can be queried in entrez 3D domains index (with field aliases in square brackets; pick one alias that's easily memorized in case multiple aliases are available):
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Updated 1/11/2005 |
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