Changes

Jump to: navigation, search

ValidatorDB:Database organization

2,191 bytes added, 13:06, 3 September 2014
Synopsis page
The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. Since this is your first contact with the database, the support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs. Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies | case studies]]''.
The '''ValidatorDB''' synopsis page further provides access to various data sets of PDB-wide validations via four different tabs, namely '''Overview''', '''Details by Residue''', '''Details by PDB entry''' and '''Custom Search'''. A full description of each of these tab is given below.  Additionally, the ''synopsis page'' allows to access the validation results for specific residues of interest via the '''Quick Lookup bar''' at the bottom of the page. Simply type a comma separated list of residue annotations (3-letter codes) into the '''Quick Lookup bar''', and you will be redirected to the [[ValidatorDB:Database_organization#Specifics_page | specifics page]] containing validation results for the molecules you requested. If you specify a list of PDB IDs (4-letter codes) instead, then the corresponding [[ValidatorDB:Database_organization#Specifics_page | specifics page]] will contain validation results for all relevant molecules in the PDB entries you specified.
{| class="wikitable" border="1"
|-
|<!--Col1-->[[File:VDB_intro.png| 750px| '''Overview''' tab]] |<!--Col2--><center>[[File:VDB_overviewVDB_samples.png| 750px| '''Summary''' tab]]</center>
|-
|<!--Col1-->1 The '''Synopsis page''' contains a general description, and is organized in 6 tabs, namely ''Quick Help'', ''Samples'', ''Overview'', ''Details by Residue'', ''Details by PDB Entry'' and ''Custom Search''. These tabs provide access to graphical and tabular overviews and statistical evaluation of validation results for the entire PDB, for each residue across all PDB IDs containing that residue, and for all analyzed residues in each PDB ID, respectively. Click on each tab to discover what type of overview can be accessed. Whenever you are unsure about the meaning of individual graphical elements either hover mouse over it or click the green '? Guide' button.
|<!--Col2-->2. The '''Samples page''' contains several examples with a short description of validation results of both validated residues and PDB entries.
|}
<br style="clearAdditionally, the ''synopsis page'' allows to access the validation results for specific residues of interest via the '''Quick Lookup bar''' at the bottom of the page. Simply type a comma separated list of residue annotations (3-letter codes) into the '''Quick Lookup bar''', and you will be redirected to the [[ValidatorDB:both" />Database_organization#Specifics_page | specifics page]] containing validation results for the molecules you requested. If you specify a list of PDB IDs (4-letter codes) instead, then the corresponding [[ValidatorDB:Database_organization#Specifics_page | specifics page]] will contain validation results for all relevant molecules in the PDB entries you specified.  
====Overview====
[[File:VDB_overview.png|thumb|right|500px|The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs.]]
 
The Overview tab of the synopsis page provides a very general statistical evaluation of results across the entire PDB in graphical form. The elements of the graph represent percentages of the total number of motifs (over 200,000) of residues relevant for validation. A graphic element will be displayed in the '''Overview''' graph only if it represents at least 0.5% of the total number of motifs. Each element of the graph is described in a tool tip, but note that here the term residue actually refers to occurrence of residue (motif).
====Details by Residue====
 
[[File:VDB_Residues.PNG|thumb|right|500px|The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs.]]
 
 
The '''Details by Residue''' tab contains an interactive table summarizing the results for each residue validated across the entire PDB. Each row corresponds to one residue, identified by its residue name (3-letter code). The information in the table is organized according to the [[ValidatorDB:Analysis_of_Results|validation result]]. The color coding for the table header and the font inside the table is the same as in the categories defined in the '''Overview''' tab. Each element of the table header is described in a tool tip, but note that here the term residue actually refers to occurrence of residue (motif).
The filter at the top right corner allows to retrieve the table row with a specific residue. Simply type the residue name into the filter. All results can be downloaded in *.csv format using the download button at the top left corner.
[[File:VDB_Residues.PNG|thumb|750px|center]]
====Details by PDB entry====
====Details [[File:VDB_PDBEntries.PNG|thumb|right|500px|The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by PDB entry====a green button at the top right corner of some tabs.]]
The '''Details by PDB Entry''' tab contains an interactive table summarizing the results for all residues validated in each PDB entry. Each row corresponds to one PDB entry, identified by its PDB ID (4-letter code). The information in the table is organized according to the [[ValidatorDB:Analysis_of_Results|validation result]]. The color coding for the table header and the font inside the table is the same as in the categories defined in the '''Overview''' tab. Each element of the table header is described in a tool tip, but note that here the term residue actually refers to occurrence of residue (motif).
The filter at the top right corner allows to retrieve the table rows with a specific residue, or the table rows with selected PDB IDs. Simply type the residue name or PDB ID into the filter. All results can be downloaded in .csv format using the download button at the top left corner.
 
[[File:VDB_PDBEntries.PNG|thumb|750px|center]]
====Custom Search====
[[File:VDB_Custom.PNG|thumb|right|500px|The ''synopsis page'Custom Search''' tab allows you consists of 6 tabs, two providing support, and four enabling access to create your own view of the ligands validation of the PDB databaseitself. Simply paste a list of your desired ligands (3-letter code) and/or PDB entries (4-letter code) in provided text boxes separated by commas or a newlines. This is particularly convenient in case you need to retrieve a validation report for a huge number of structures. Such as all the The support tabs '''Quick Help'''glycosyltransferasesand '' or 'Samples'nmr structures''. Note that help you can retrieve such lists by using [http://www.rcsb.org/pdb/search/advSearch.do advanced search in PDB]. Also bear in mind that each get started, with basic information and examples of these custom searches will be assigned a unique permanent web address, so you can access these results later ondatabase snippets. Also Various interactive guides are accessible by a list green button at the top right corner of your last custom searches is provided for your convenientsome tabs. ]]
The '''Custom Search''' tab allows you to create your own view of the ligands validation of the PDB database. Simply paste a list of your desired ligands (3-letter code) and/or PDB entries (4-letter code) in provided text boxes separated by commas or a newlines. This is particularly convenient in case you need to retrieve a validation report for a huge number of structures. Such as all the ''glycosyltransferases'' or ''nmr structures''. Note that you can retrieve such lists by using [[Filehttp:VDB_Custom//www.PNG|thumb|750px|center]rcsb.org/pdb/search/advSearch.do advanced search in PDB]. Also bear in mind that each of these custom searches will be assigned a unique permanent web address, so you can access these results later on. Also a list of your last custom searches is provided for your convenient.
=Specifics page=

Navigation menu