ValidatorDB:Database organization - Revision history

Lukas: /* Synopsis page */

2014-12-28T10:03:54Z

Synopsis page

← Older revision		Revision as of 10:03, 28 December 2014
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	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 ''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]]''.

	{\| class="wikitable" border="1" style="margin: 1em auto 1em auto;"		{\| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
	\|-		\|-
	\|<!--Col1--><center>[[File:VDB_intro.png\| 650px]]		\|<!--Col1--><center>[[File:VDB_intro.png\| 650px]]
	\|<!--Col2-->[[File:VDB_samples.png\| 650px]]		\|<!--Col2-->[[File:VDB_samples.png\| 650px]]
	\|-		\|-
	\|<!--Col1-->The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. ~~<br />~~The support tab '''Quick Help''' helps you get started, with basic information about how to get oriented in the~~<br />~~ web page. Various interactive guides are accessible by a green button at the top right corner of some tabs.~~<br />~~ Tool tips are available for most of the graphical elements.		\|<!--Col1-->The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tab '''Quick Help''' helps you get started, with basic information about how to get oriented in the web page. Various interactive guides are accessible by a green button at the top right corner of some tabs. Tool tips are available for most of the graphical elements.
	\|<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a brief interpretation of results. Two categories of sample validation reports (Molecules, PDB Entry) illustrate interesting cases of molecules with a high or low number of errors. Additionally, the Step-by-Step category contains video tutorials and slides explaining how to obtain such results. Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies \| case studies]]''.		\|<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a brief interpretation of results. Two categories of sample validation reports (Molecules, PDB Entry) illustrate interesting cases of molecules with a high or low number of errors. Additionally, the Step-by-Step category contains video tutorials and slides explaining how to obtain such results. Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies \| case studies]]''.
	\|}		\|}

Crina: /* Processing Warnings */

2014-10-20T22:16:41Z

Processing Warnings

← Older revision		Revision as of 22:16, 20 October 2014
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	<br style="clear:both" />		<br style="clear:both" />

	'''Continue by examining the [[ValidatorDB:~~Case_studies~~ \| case studies]], or return to the [[ValidatorDB:UserManual \| Table of contents]].'''		'''Continue by examining the [[ValidatorDB:CaseStudies \| case studies]], or return to the [[ValidatorDB:UserManual \| Table of contents]].'''

Crina: /* Processing Warnings */

2014-10-20T22:15:37Z

Processing Warnings

← Older revision		Revision as of 22:15, 20 October 2014
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	<br style="clear:both" />		<br style="clear:both" />

	'''Continue by ~~learning about~~ the [[ValidatorDB:~~Database_organization~~ \| ~~organization~~]] ~~of ValidatorDB~~, or return to the [[ValidatorDB:UserManual \| Table of contents]].'''		'''Continue by examining the [[ValidatorDB:Case_studies \| case studies]], or return to the [[ValidatorDB:UserManual \| Table of contents]].'''

Crina: /* Processing Warnings */

2014-10-20T22:13:17Z

Processing Warnings

← Older revision		Revision as of 22:13, 20 October 2014
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	The drop down menu at the top of the page helps filter the warnings for molecules with a specific annotation (3-letter code).		The drop down menu at the top of the page helps filter the warnings for molecules with a specific annotation (3-letter code).
	<br style="clear:both" />		<br style="clear:both" />

			'''Continue by learning about the [[ValidatorDB:Database_organization \| organization]] of ValidatorDB, or return to the [[ValidatorDB:UserManual \| Table of contents]].'''

Crina: /* Search */

2014-10-20T22:02:37Z

← Older revision		Revision as of 22:02, 20 October 2014
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	==Search==		==Search==

	[[File:ValidatorDB-Search By Entry and Annotation.png\|thumb\|right\|~~500px~~\|The '''Search tab''' allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.]]		[[File:ValidatorDB-Search By Entry and Annotation.png\|thumb\|right\|650px\|The '''Search tab''' allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.]]

	'''ValidatorDB''' contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The ''synopsis page'' allows to access specific validation reports via the '''Search tab'''.		'''ValidatorDB''' contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The ''synopsis page'' allows to access specific validation reports via the '''Search tab'''.

Crina: /* Search */

2014-10-20T22:02:13Z

← Older revision		Revision as of 22:02, 20 October 2014
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	==Search==		==Search==

	[[File:ValidatorDB-Search By Entry and Annotation.png\|thumb\|right\|~~650px~~\|The '''Search tab''' allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.]]		[[File:ValidatorDB-Search By Entry and Annotation.png\|thumb\|right\|500px\|The '''Search tab''' allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.]]

	'''ValidatorDB''' contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The ''synopsis page'' allows to access specific validation reports via the '''Search tab'''.		'''ValidatorDB''' contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The ''synopsis page'' allows to access specific validation reports via the '''Search tab'''.
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	Click on criterion you plan to use. In each case, there will be an input field where you can enter a comma or new line separated list of values for the relevant criterion. You may prefer to use the advanced search functions available on the Protein Data Bank web page, in order to generate a list of relevant annotations and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.		Click on criterion you plan to use. In each case, there will be an input field where you can enter a comma or new line separated list of values for the relevant criterion. You may prefer to use the advanced search functions available on the Protein Data Bank web page, in order to generate a list of relevant annotations and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.

	~~The~~ validation results for the molecules you specified according to the chosen criteria are then retrieved from '''ValidatorDB''', organized and made accessible via a unique ''[[ValidatorDB:Database_organization#Specifics_page \| specifics page]]'', which you can access at a later time via its unique URL. The ''[[ValidatorDB:Database_organization#Specifics_page \| specifics page]]'' is described in detail in the second part of the ''Data organization'' section of this manual.		Once you click the blue search button at the bottom of the page, the validation results for the molecules you specified according to the chosen criteria are then retrieved from '''ValidatorDB''', organized and made accessible via a unique ''[[ValidatorDB:Database_organization#Specifics_page \| specifics page]]'', which you can access at a later time via its unique URL. The ''[[ValidatorDB:Database_organization#Specifics_page \| specifics page]]'' is described in detail in the second part of the ''Data organization'' section of this manual.

	The last 10 searches you performed are listed for your convenience.		The last 10 searches you performed are listed for your convenience.

Crina: /* Custom search */

2014-10-20T21:57:23Z

Custom search

← Older revision		Revision as of 21:57, 20 October 2014
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	==~~Custom search~~==		==Search==

	[[File:~~VDB_Custom~~.~~PNG~~\|thumb\|right\|650px\|The '''~~Custom search~~ tab''' allows to retrieve validation reports for specific molecules, ~~according to~~ annotation (3-letter code) ~~and~~ PDB entry.]]		[[File:ValidatorDB-Search By Entry and Annotation.png\|thumb\|right\|650px\|The '''Search tab''' allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.]]

	~~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~~.		'''ValidatorDB''' contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The ''synopsis page'' allows to access specific validation reports via the '''Search tab'''.

	~~In addition to~~ the ~~predefined summaries and reports already described~~, ~~'''ValidatorDB''' can generate custom validation reports using the '''Custom Search''' functionality. Such custom validator reports allow you better focus on molecules of interest~~ (~~drug molecules~~, ~~polycyclic molecules~~, ~~etc.~~), ~~from relevant~~ PDB ~~entries (entries with a resolution higher than 2 Å~~, ~~published after 2010, etc.)~~.		You may define the search using several criteria, namely PDB entry (4-letter code), molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation. The syntax of the search is quite simple, but you can always check out the examples and tool tips if you want to make sure.

	~~You may specify~~ a ~~set~~ of ~~molecules using PDB IDs (4-letter codes) and annotations (3-letter codes)~~. ~~Alternatively, you~~ may prefer to use the advanced search functions available on the Protein Data Bank web page, in order to generate a list of relevant annotations and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.		Click on criterion you plan to use. In each case, there will be an input field where you can enter a comma or new line separated list of values for the relevant criterion. You may prefer to use the advanced search functions available on the Protein Data Bank web page, in order to generate a list of relevant annotations and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.

	The validation results for the molecules you specified are then retrieved from '''ValidatorDB''', organized and made accessible ~~in the same manner as the above described tabs, namely '~~''[[ValidatorDB:Database_organization#~~Overview~~ \| ~~Overview~~]]''', '''[[ValidatorDB:Database_organization#~~Details_by_molecule~~ \| ~~Details by molecule~~]]'''~~, and~~ '''~~[[ValidatorDB:Database_organization#Details_by_PDB_entry \| Details by PDB entry]]'''. The only difference is that the statistics will refer to your selection, and not to the entire PDB. Moreover,~~ this ~~custom snippet of the database will be accessible at its own URL for some time, so that you can return to it later on~~. The last 10 searches you performed are listed for your convenience.		The validation results for the molecules you specified according to the chosen criteria are then retrieved from '''ValidatorDB''', organized and made accessible via a unique ''[[ValidatorDB:Database_organization#Specifics_page \| specifics page]]'', which you can access at a later time via its unique URL. The ''[[ValidatorDB:Database_organization#Specifics_page \| specifics page]]'' is described in detail in the second part of the ''Data organization'' section of this manual.

			The last 10 searches you performed are listed for your convenience.

Crina at 21:18, 20 October 2014

2014-10-20T21:18:55Z

@@ Line 15: / Line 15: @@
   |-
   |<!--Col1-->The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. <br />The support tab '''Quick Help''' helps you get started, with basic information about how to get oriented in the<br /> web page. Various interactive guides are accessible by a green button at the top right corner of some tabs.<br /> Tool tips are available for most of the graphical elements.
-  |<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a brief interpretation of results.<br /> Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies | case studies]]''.
+  |<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a brief interpretation of results. Two categories of sample validation reports (Molecules, PDB Entry) illustrate interesting cases of molecules with a high or low number of errors. Additionally, the Step-by-Step category contains video tutorials and slides explaining how to obtain such results. 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 '''[[ValidatorDB:Database_organization#Overview | Overview]]''', '''[[ValidatorDB:Database_organization#Details_by_molecule | Details by molecule]]''',  '''[[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry]]''' and  '''[[ValidatorDB:Database_organization#Custom_search | Custom search]]'''. A full description of each of these tab is given in their respective sections.
+The '''ValidatorDB''' synopsis page further provides access to various data sets. You may retrieve specific validation reports using the '''[[ValidatorDB:Database_organization#Search | Search]]''' tab. Further, the results from PDB-wide validations are available via three different tabs, namely '''[[ValidatorDB:Database_organization#Overview | Overview]]''', '''[[ValidatorDB:Database_organization#Details_by_molecule | Details by molecule]]''' and '''[[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry]]'''. A full description of each of these tab is given in their respective sections.
 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.
 ==Overview==
@@ Line 64: / Line 78: @@
 The results for different types of validation analyses are labeled using the unified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, <span style="color:#DAA520">wrong chirality</span>, <span style="color:#607d8b">warning</span>.
 <br style="clear:both" />

Lukas: /* Summary */

2014-10-20T19:06:33Z

Summary

← Older revision		Revision as of 19:06, 20 October 2014
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	The validation reports available in the '''Summary''' tab of the ''specifics page'' are organized by annotation (3-letter code). You can easily navigate between reports by clicking on the annotation of interest in the bar under the tab names. Each report consists of information about the model and validated molecules corresponding to that particular annotation.		The validation reports available in the '''Summary''' tab of the ''specifics page'' are organized by annotation (3-letter code). You can easily navigate between reports by clicking on the annotation of interest in the bar under the tab names. Each report consists of information about the model and validated molecules corresponding to that particular annotation.

	{\| class="wikitable" border="1"		{\| class="wikitable" border="1" style="margin: 1em auto 1em auto;"
	\|-		\|-
	\|<!--Col1-->[[File:VDB_Residue_summary.PNG\| ~~500px~~]]		\|<!--Col1-->[[File:VDB_Residue_summary.PNG\| 650px]]
	\|<!--Col2-->[[File:VDB_Entry_summary.PNG\| ~~500px~~]]		\|<!--Col2-->[[File:VDB_Entry_summary.PNG\| 650px]]
	\|-		\|-
	\|<!--Col1-->The '''Summary''' tab of the ''specifics page'' for all molecules sharing a '''specific annotation (3-letter code)'''. The report consists of a description of the model corresponding to that annotation, a recapitulation of all validated molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced), and statistics for each problematic atom.		\|<!--Col1-->The '''Summary''' tab of the ''specifics page'' for all molecules sharing a '''specific annotation (3-letter code)'''. The<br/> report consists of a description of the model corresponding to that annotation, a recapitulation of all validated<br/> molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced),<br/> and statistics for each problematic atom.
	\|<!--Col2--> The '''Summary''' tab of the ''specifics page'' for a '''single PDB entry''' allows easy navigation between annotation-based validation reports. Each report consists of a description of the model corresponding to that annotation, a recapitulation of all validated molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced), and statistics for each problematic atom.		\|<!--Col2--> The '''Summary''' tab of the ''specifics page'' for a '''single PDB entry''' allows easy navigation between annotation-based<br/> validation reports. Each report consists of a description of the model corresponding to that annotation,<br/> a recapitulation of all validated molecules sharing that annotation, statistics for each validation analysis<br/> (completeness, chirality, advanced), and statistics for each problematic atom.
	\|}		\|}

Lukas: /* Synopsis page */

2014-10-20T19:03:31Z

Synopsis page

← Older revision		Revision as of 19:03, 20 October 2014
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	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 ''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]]''.

	{\| class="wikitable" border="1"		{\| class="wikitable" border="1" style="margin: 1em auto 1em auto;"
	\|-		\|-
	\|<!--Col1--><center>[[File:VDB_intro.png\| 650px]]		\|<!--Col1--><center>[[File:VDB_intro.png\| 650px]]
	\|<!--Col2-->[[File:VDB_samples.png\| ~~500px~~]]		\|<!--Col2-->[[File:VDB_samples.png\| 650px]]
	\|-		\|-
	\|<!--Col1-->The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tab '''Quick Help''' helps you get started, with basic information about how to get oriented in the web page. Various interactive guides are accessible by a green button at the top right corner of some tabs. Tool tips are available for most of the graphical elements.		\|<!--Col1-->The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. <br />The support tab '''Quick Help''' helps you get started, with basic information about how to get oriented in the<br /> web page. Various interactive guides are accessible by a green button at the top right corner of some tabs.<br /> Tool tips are available for most of the graphical elements.
	\|<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a brief interpretation of results. Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies \| case studies]]''.		\|<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a brief interpretation of results.<br /> Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies \| case studies]]''.
	\|}		\|}