PatternQuery:UserManual - Revision history

Lukas: /* Using PatternQuery Service */

2015-04-27T09:15:17Z

Using PatternQuery Service

← Older revision		Revision as of 09:15, 27 April 2015
Line 41:		Line 41:
	# [[PatternQuery:Specifics Page\| Specifics Page (result analysis)]]		# [[PatternQuery:Specifics Page\| Specifics Page (result analysis)]]
	## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[PatternQuery:Specifics Page#~~Fragment~~ Details \| ~~Fragment~~ Details]]		## [[PatternQuery:Specifics Page#Pattern Details \| Pattern Details]]
	## [[PatternQuery:Specifics Page#Structure Details \| Structure Details ]]		## [[PatternQuery:Specifics Page#Structure Details \| Structure Details ]]
	----		----

Lukas: /* Using PatternQuery Service */

2015-04-27T09:14:01Z

Using PatternQuery Service

← Older revision		Revision as of 09:14, 27 April 2015
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	# [[PatternQuery:Service Organization#Synopsis Page \| Synopsis Page]]		# [[PatternQuery:Service Organization#Synopsis Page \| Synopsis Page]]
	# [[PatternQuery:Service Organization#Job Submission \| Job submission]]		# [[PatternQuery:Service Organization#Job Submission \| Job submission]]
	~~# [[PatternQuery:Service Organization#Specifics Page \| Result analysis]]~~		# [[PatternQuery:Specifics Page\| Specifics Page (result analysis)]]
	# [[PatternQuery:Specifics Page\| Specifics Page]]
	## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[PatternQuery:Specifics Page#Fragment Details \| Fragment Details]]		## [[PatternQuery:Specifics Page#Fragment Details \| Fragment Details]]

Dave at 22:23, 26 April 2015

2015-04-26T22:23:19Z

← Older revision		Revision as of 22:23, 26 April 2015
Line 3:		Line 3:
	'''PatternQuery''' ('''PQ''') is interactive, user-friendly and platform independent web service enabling users to effectively define, extract and analyze biomolecular structural patterns using the '''PatternQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.		'''PatternQuery''' ('''PQ''') is interactive, user-friendly and platform independent web service enabling users to effectively define, extract and analyze biomolecular structural patterns using the '''PatternQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.

	'''PQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller datasets can be processed by the [[PatternQuery:~~MotiveExplorer~~ \| PatternQuery Explorer]] application. Larger in-house databases can be processed with the [[PatternQuery:Command Line \| command line application]].		'''PQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller datasets can be processed by the [[PatternQuery:Explorer \| PatternQuery Explorer]] application. Larger in-house databases can be processed with the [[PatternQuery:Command Line \| command line application]].

	Below you can find the '''PQ''' user manual, which contains all the information you need in order to make efficient use of '''PQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/PatternQuery/Index '''PQ''' web pages]. When you first access the '''PQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.		Below you can find the '''PQ''' user manual, which contains all the information you need in order to make efficient use of '''PQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/PatternQuery/Index '''PQ''' web pages]. When you first access the '''PQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.

Lukas: /* PatternQuery Explorer */

2015-04-25T12:59:16Z

PatternQuery Explorer

← Older revision		Revision as of 12:59, 25 April 2015
Line 30:		Line 30:
	#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]		#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]
	----		----
	===[[PatternQuery:~~MotiveExplorer~~ \| PatternQuery Explorer]]===		===[[PatternQuery:Explorer \| PatternQuery Explorer]]===
	# [[PatternQuery:~~MotiveExplorer~~#Launch PatternQuery Explorer app \| Launch application]]		# [[PatternQuery:Explorer#Launch PatternQuery Explorer app \| Launch application]]
	# [[PatternQuery:~~MotiveExplorer~~#Get started with PatternQuery Explorer \| How to work with it]]		# [[PatternQuery:Explorer#Get started with PatternQuery Explorer \| How to work with it]]
	# [[PatternQuery:~~MotiveExplorer~~#Executing Query & interpreting results \| Execute query]]		# [[PatternQuery:Explorer#Executing Query & interpreting results \| Execute query]]
	----		----

Lukas at 12:54, 25 April 2015

2015-04-25T12:54:59Z

← Older revision		Revision as of 12:54, 25 April 2015
Line 1:		Line 1:
	__NOTOC__		__NOTOC__

	'''~~MotiveQuery~~''' ('''MQ''') is interactive, user-friendly and platform independent web service enabling users to effectively define, extract and analyze biomolecular structural ~~fragments~~ using the '''~~MotiveQuery~~ language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.		'''PatternQuery''' ('''PQ''') is interactive, user-friendly and platform independent web service enabling users to effectively define, extract and analyze biomolecular structural patterns using the '''PatternQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.

	'''MQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller datasets can be processed by the [[~~MotiveQuery~~:MotiveExplorer \| ~~MotiveQuery~~ Explorer]] application. Larger in-house databases can be processed with the [[~~MotiveQuery~~:Command Line \| command line application]].		'''PQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller datasets can be processed by the [[PatternQuery:MotiveExplorer \| PatternQuery Explorer]] application. Larger in-house databases can be processed with the [[PatternQuery:Command Line \| command line application]].

	Below you can find the '''MQ''' user manual, which contains all the information you need in order to make efficient use of '''MQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/~~MotiveQuery~~/Index '''MQ''' web pages]. When you first access the '''MQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.		Below you can find the '''PQ''' user manual, which contains all the information you need in order to make efficient use of '''PQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/PatternQuery/Index '''PQ''' web pages]. When you first access the '''PQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.
	----		----
	===[[~~MotiveQuery~~:Introduction \| Introduction]]===		===[[PatternQuery:Introduction \| Introduction]]===
	----		----
	===[[~~MotiveQuery~~:Terminology \| Terminology]]===		===[[PatternQuery:Terminology \| Terminology]]===
	#[[~~MotiveQuery~~:Terminology#Atom \| Atom]]		#[[PatternQuery:Terminology#Atom \| Atom]]
	#[[~~MotiveQuery~~:Terminology#Residue \| Residue]]		#[[PatternQuery:Terminology#Residue \| Residue]]
	#[[~~MotiveQuery~~:Terminology#Fragment \| Fragment]]		#[[PatternQuery:Terminology#Fragment \| Fragment]]
	#[[~~MotiveQuery~~:Terminology#Query \| Query]]		#[[PatternQuery:Terminology#Query \| Query]]

	----		----
	===[[~~MotiveQuery~~:Principles \| Principles of the MQ language]]===		===[[PatternQuery:Principles \| Principles of the PQ language]]===
	#[[~~MotiveQuery~~:Principles#Example, Part One \| Example - introduction]]		#[[PatternQuery:Principles#Example, Part One \| Example - introduction]]
	#[[~~MotiveQuery~~:Principles#Basic Principles of the Language \| Basic Principle]]		#[[PatternQuery:Principles#Basic Principles of the Language \| Basic Principle]]
	#[[~~MotiveQuery~~:Principles#Example, Part One \| Example - revised]]		#[[PatternQuery:Principles#Example, Part One \| Example - revised]]
	----		----
	===[[~~MotiveQuery~~:How to build a query \| How to build a query]]===		===[[PatternQuery:How to build a query \| How to build a query]]===
	#[[~~MotiveQuery~~:How to build a query#How to think about queries \| How to think about query]]		#[[PatternQuery:How to build a query#How to think about queries \| How to think about query]]
	#[[~~MotiveQuery~~:How to build a query#Ready-to-use examples \| Ready-to-use examples]]		#[[PatternQuery:How to build a query#Ready-to-use examples \| Ready-to-use examples]]
	----		----
	===[[~~MotiveQuery~~:Use Cases \| Biological use cases]]===		===[[PatternQuery:Use Cases \| Biological use cases]]===
	#[[~~MotiveQuery~~:Use Cases#Find all post-translational modified amino acids \| Post-translational modified aminoacids]]		#[[PatternQuery:Use Cases#Find all post-translational modified amino acids \| Post-translational modified aminoacids]]
	#[[~~MotiveQuery~~:Use Cases#Identify Zinc fingers \| Zinc fingers]]		#[[PatternQuery:Use Cases#Identify Zinc fingers \| Zinc fingers]]
	#[[~~MotiveQuery~~:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]		#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]
	----		----
	===[[~~MotiveQuery~~:MotiveExplorer \| ~~MotiveQuery~~ Explorer]]===		===[[PatternQuery:MotiveExplorer \| PatternQuery Explorer]]===
	# [[~~MotiveQuery~~:MotiveExplorer#Launch ~~MotiveQuery~~ Explorer app \| Launch application]]		# [[PatternQuery:MotiveExplorer#Launch PatternQuery Explorer app \| Launch application]]
	# [[~~MotiveQuery~~:MotiveExplorer#Get started with ~~MotiveQuery~~ Explorer \| How to work with it]]		# [[PatternQuery:MotiveExplorer#Get started with PatternQuery Explorer \| How to work with it]]
	# [[~~MotiveQuery~~:MotiveExplorer#Executing Query & interpreting results \| Execute query]]		# [[PatternQuery:MotiveExplorer#Executing Query & interpreting results \| Execute query]]
	----		----

	===[[~~MotiveQuery~~:Service Organization \| Using ~~MotiveQuery~~ Service]]===		===[[PatternQuery:Service Organization \| Using PatternQuery Service]]===
	# [[~~MotiveQuery~~:Service Organization#Synopsis Page \| Synopsis Page]]		# [[PatternQuery:Service Organization#Synopsis Page \| Synopsis Page]]
	# [[~~MotiveQuery~~:Service Organization#Job Submission \| Job submission]]		# [[PatternQuery:Service Organization#Job Submission \| Job submission]]
	# [[~~MotiveQuery~~:Service Organization#Specifics Page \| Result analysis]]		# [[PatternQuery:Service Organization#Specifics Page \| Result analysis]]
	# [[~~MotiveQuery~~:Specifics Page\| Specifics Page]]		# [[PatternQuery:Specifics Page\| Specifics Page]]
	## [[~~MotiveQuery~~:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[~~MotiveQuery~~:Specifics Page#Fragment Details \| Fragment Details]]		## [[PatternQuery:Specifics Page#Fragment Details \| Fragment Details]]
	## [[~~MotiveQuery~~:Specifics Page#Structure Details \| Structure Details ]]		## [[PatternQuery:Specifics Page#Structure Details \| Structure Details ]]
	----		----

	===[[~~MotiveQuery~~:Language_Reference \| Language reference]]===		===[[PatternQuery:Language_Reference \| Language reference]]===
	----		----
	===[[~~MotiveQuery~~:Command Line \| Command line version & Technical details]]===		===[[PatternQuery:Command Line \| Command line version & Technical details]]===
	----		----

Lukas: Lukas moved page MotiveQuery:UserManual to PatternQuery:UserManual: Change of the service name

2015-04-25T12:43:47Z

Lukas moved page MotiveQuery:UserManual to PatternQuery:UserManual: Change of the service name

← Older revision	Revision as of 12:43, 25 April 2015
(No difference)

Lukas: /* Using MotiveQuery Service */

2015-04-20T15:40:05Z

Using MotiveQuery Service

← Older revision		Revision as of 15:40, 20 April 2015
Line 40:		Line 40:
	# [[MotiveQuery:Service Organization#Job Submission \| Job submission]]		# [[MotiveQuery:Service Organization#Job Submission \| Job submission]]
	# [[MotiveQuery:Service Organization#Specifics Page \| Result analysis]]		# [[MotiveQuery:Service Organization#Specifics Page \| Result analysis]]
			# [[MotiveQuery:Specifics Page\| Specifics Page]]
	## [[MotiveQuery:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[MotiveQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[MotiveQuery:Specifics Page#Fragment Details \| Fragment Details]]		## [[MotiveQuery:Specifics Page#Fragment Details \| Fragment Details]]

Lukas at 14:03, 20 April 2015

2015-04-20T14:03:06Z

← Older revision		Revision as of 14:03, 20 April 2015
Line 1:		Line 1:
	__NOTOC__		__NOTOC__

	'''MotiveQuery''' ('''MQ''') is interactive, user-friendly and platform independent web service enabling ~~user~~ to effectively define, extract and analyze biomolecular structural fragments using '''MotiveQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.		'''MotiveQuery''' ('''MQ''') is interactive, user-friendly and platform independent web service enabling users to effectively define, extract and analyze biomolecular structural fragments using the '''MotiveQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.

	~~The~~ '''MQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller ~~amount of user structures~~ can be processed in the [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] application. Larger in-house databases can be processed with the [[MotiveQuery:Command Line \| command line application]].		'''MQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller datasets can be processed by the [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] application. Larger in-house databases can be processed with the [[MotiveQuery:Command Line \| command line application]].

	Below you can find the '''MQ''' user manual, which contains all the information you need in order to make efficient use of '''MQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index '''MQ''' web pages]. When you first access the '''MQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.		Below you can find the '''MQ''' user manual, which contains all the information you need in order to make efficient use of '''MQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index '''MQ''' web pages]. When you first access the '''MQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.

Lukas: /* Using MotiveQuery Service */

2014-12-28T13:05:31Z

Using MotiveQuery Service

← Older revision		Revision as of 13:05, 28 December 2014
Line 39:		Line 39:
	# [[MotiveQuery:Service Organization#Synopsis Page \| Synopsis Page]]		# [[MotiveQuery:Service Organization#Synopsis Page \| Synopsis Page]]
	# [[MotiveQuery:Service Organization#Job Submission \| Job submission]]		# [[MotiveQuery:Service Organization#Job Submission \| Job submission]]
	# [[MotiveQuery:Service Organization#Specifics Page\| Result analysis]]		# [[MotiveQuery:Service Organization#Specifics Page \| Result analysis]]
			## [[MotiveQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
			## [[MotiveQuery:Specifics Page#Fragment Details \| Fragment Details]]
			## [[MotiveQuery:Specifics Page#Structure Details \| Structure Details ]]
	----		----

Lukas at 10:01, 28 December 2014

2014-12-28T10:01:49Z

← Older revision		Revision as of 10:01, 28 December 2014
Line 3:		Line 3:
	'''MotiveQuery''' ('''MQ''') is interactive, user-friendly and platform independent web service enabling user to effectively define, extract and analyze biomolecular structural fragments using '''MotiveQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.		'''MotiveQuery''' ('''MQ''') is interactive, user-friendly and platform independent web service enabling user to effectively define, extract and analyze biomolecular structural fragments using '''MotiveQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.

	The '''MQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller amount of user structures can be processed in the [[MotiveQuery:MotiveExplorer \| ~~MotiveExplorer~~]] application. Larger in-house databases can be processed with the [[MotiveQuery:Command Line \| command line application]].		The '''MQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller amount of user structures can be processed in the [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] application. Larger in-house databases can be processed with the [[MotiveQuery:Command Line \| command line application]].

	Below you can find the '''MQ''' user manual, which contains all the information you need in order to make efficient use of '''MQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index '''MQ''' web pages]. When you first access the '''MQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.		Below you can find the '''MQ''' user manual, which contains all the information you need in order to make efficient use of '''MQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index '''MQ''' web pages]. When you first access the '''MQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.

← Older revision		Revision as of 09:15, 27 April 2015
Line 41:		Line 41:
	# [[PatternQuery:Specifics Page\| Specifics Page (result analysis)]]		# [[PatternQuery:Specifics Page\| Specifics Page (result analysis)]]
	## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[PatternQuery:Specifics Page#~~Fragment~~ Details \| ~~Fragment~~ Details]]		## [[PatternQuery:Specifics Page#Pattern Details \| Pattern Details]]
	## [[PatternQuery:Specifics Page#Structure Details \| Structure Details ]]		## [[PatternQuery:Specifics Page#Structure Details \| Structure Details ]]
	----		----

← Older revision		Revision as of 09:14, 27 April 2015
Line 39:		Line 39:
	# [[PatternQuery:Service Organization#Synopsis Page \| Synopsis Page]]		# [[PatternQuery:Service Organization#Synopsis Page \| Synopsis Page]]
	# [[PatternQuery:Service Organization#Job Submission \| Job submission]]		# [[PatternQuery:Service Organization#Job Submission \| Job submission]]
	~~# [[PatternQuery:Service Organization#Specifics Page \| Result analysis]]~~		# [[PatternQuery:Specifics Page\| Specifics Page (result analysis)]]
	# [[PatternQuery:Specifics Page\| Specifics Page]]
	## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[PatternQuery:Specifics Page#Fragment Details \| Fragment Details]]		## [[PatternQuery:Specifics Page#Fragment Details \| Fragment Details]]

← Older revision		Revision as of 12:59, 25 April 2015
Line 30:		Line 30:
	#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]		#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]
	----		----
	===[[PatternQuery:~~MotiveExplorer~~ \| PatternQuery Explorer]]===		===[[PatternQuery:Explorer \| PatternQuery Explorer]]===
	# [[PatternQuery:~~MotiveExplorer~~#Launch PatternQuery Explorer app \| Launch application]]		# [[PatternQuery:Explorer#Launch PatternQuery Explorer app \| Launch application]]
	# [[PatternQuery:~~MotiveExplorer~~#Get started with PatternQuery Explorer \| How to work with it]]		# [[PatternQuery:Explorer#Get started with PatternQuery Explorer \| How to work with it]]
	# [[PatternQuery:~~MotiveExplorer~~#Executing Query & interpreting results \| Execute query]]		# [[PatternQuery:Explorer#Executing Query & interpreting results \| Execute query]]
	----		----

← Older revision		Revision as of 12:54, 25 April 2015
Line 1:		Line 1:
	__NOTOC__		__NOTOC__

	'''~~MotiveQuery~~''' ('''MQ''') is interactive, user-friendly and platform independent web service enabling users to effectively define, extract and analyze biomolecular structural ~~fragments~~ using the '''~~MotiveQuery~~ language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.		'''PatternQuery''' ('''PQ''') is interactive, user-friendly and platform independent web service enabling users to effectively define, extract and analyze biomolecular structural patterns using the '''PatternQuery language'''. Such analysis is particularly useful not only in a structural and functional assignment of uncharacterized or newly determined proteins, but also represents a key point in rational design and engineering of novel functional sites and comparative protein structural analyses.

	'''MQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller datasets can be processed by the [[~~MotiveQuery~~:MotiveExplorer \| ~~MotiveQuery~~ Explorer]] application. Larger in-house databases can be processed with the [[~~MotiveQuery~~:Command Line \| command line application]].		'''PQ''' is provided as a web service for mining the whole [http://pdb.org/pdb/home/home.do PDB database], however it can also be restricted based on numerous metadata, such as the ''Release date'', ''Resolution'', ''EC number'' and so on. Therefore, only structures relevant for your research are processed. Additionally, smaller datasets can be processed by the [[PatternQuery:MotiveExplorer \| PatternQuery Explorer]] application. Larger in-house databases can be processed with the [[PatternQuery:Command Line \| command line application]].

	Below you can find the '''MQ''' user manual, which contains all the information you need in order to make efficient use of '''MQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/~~MotiveQuery~~/Index '''MQ''' web pages]. When you first access the '''MQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.		Below you can find the '''PQ''' user manual, which contains all the information you need in order to make efficient use of '''PQ'''. Additional support is provided on the [http://webchem.ncbr.muni.cz/Platform/PatternQuery/Index '''PQ''' web pages]. When you first access the '''PQ''' page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.
	----		----
	===[[~~MotiveQuery~~:Introduction \| Introduction]]===		===[[PatternQuery:Introduction \| Introduction]]===
	----		----
	===[[~~MotiveQuery~~:Terminology \| Terminology]]===		===[[PatternQuery:Terminology \| Terminology]]===
	#[[~~MotiveQuery~~:Terminology#Atom \| Atom]]		#[[PatternQuery:Terminology#Atom \| Atom]]
	#[[~~MotiveQuery~~:Terminology#Residue \| Residue]]		#[[PatternQuery:Terminology#Residue \| Residue]]
	#[[~~MotiveQuery~~:Terminology#Fragment \| Fragment]]		#[[PatternQuery:Terminology#Fragment \| Fragment]]
	#[[~~MotiveQuery~~:Terminology#Query \| Query]]		#[[PatternQuery:Terminology#Query \| Query]]

	----		----
	===[[~~MotiveQuery~~:Principles \| Principles of the MQ language]]===		===[[PatternQuery:Principles \| Principles of the PQ language]]===
	#[[~~MotiveQuery~~:Principles#Example, Part One \| Example - introduction]]		#[[PatternQuery:Principles#Example, Part One \| Example - introduction]]
	#[[~~MotiveQuery~~:Principles#Basic Principles of the Language \| Basic Principle]]		#[[PatternQuery:Principles#Basic Principles of the Language \| Basic Principle]]
	#[[~~MotiveQuery~~:Principles#Example, Part One \| Example - revised]]		#[[PatternQuery:Principles#Example, Part One \| Example - revised]]
	----		----
	===[[~~MotiveQuery~~:How to build a query \| How to build a query]]===		===[[PatternQuery:How to build a query \| How to build a query]]===
	#[[~~MotiveQuery~~:How to build a query#How to think about queries \| How to think about query]]		#[[PatternQuery:How to build a query#How to think about queries \| How to think about query]]
	#[[~~MotiveQuery~~:How to build a query#Ready-to-use examples \| Ready-to-use examples]]		#[[PatternQuery:How to build a query#Ready-to-use examples \| Ready-to-use examples]]
	----		----
	===[[~~MotiveQuery~~:Use Cases \| Biological use cases]]===		===[[PatternQuery:Use Cases \| Biological use cases]]===
	#[[~~MotiveQuery~~:Use Cases#Find all post-translational modified amino acids \| Post-translational modified aminoacids]]		#[[PatternQuery:Use Cases#Find all post-translational modified amino acids \| Post-translational modified aminoacids]]
	#[[~~MotiveQuery~~:Use Cases#Identify Zinc fingers \| Zinc fingers]]		#[[PatternQuery:Use Cases#Identify Zinc fingers \| Zinc fingers]]
	#[[~~MotiveQuery~~:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]		#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring \| Residue containing carbohydrate moiety]]
	----		----
	===[[~~MotiveQuery~~:MotiveExplorer \| ~~MotiveQuery~~ Explorer]]===		===[[PatternQuery:MotiveExplorer \| PatternQuery Explorer]]===
	# [[~~MotiveQuery~~:MotiveExplorer#Launch ~~MotiveQuery~~ Explorer app \| Launch application]]		# [[PatternQuery:MotiveExplorer#Launch PatternQuery Explorer app \| Launch application]]
	# [[~~MotiveQuery~~:MotiveExplorer#Get started with ~~MotiveQuery~~ Explorer \| How to work with it]]		# [[PatternQuery:MotiveExplorer#Get started with PatternQuery Explorer \| How to work with it]]
	# [[~~MotiveQuery~~:MotiveExplorer#Executing Query & interpreting results \| Execute query]]		# [[PatternQuery:MotiveExplorer#Executing Query & interpreting results \| Execute query]]
	----		----

	===[[~~MotiveQuery~~:Service Organization \| Using ~~MotiveQuery~~ Service]]===		===[[PatternQuery:Service Organization \| Using PatternQuery Service]]===
	# [[~~MotiveQuery~~:Service Organization#Synopsis Page \| Synopsis Page]]		# [[PatternQuery:Service Organization#Synopsis Page \| Synopsis Page]]
	# [[~~MotiveQuery~~:Service Organization#Job Submission \| Job submission]]		# [[PatternQuery:Service Organization#Job Submission \| Job submission]]
	# [[~~MotiveQuery~~:Service Organization#Specifics Page \| Result analysis]]		# [[PatternQuery:Service Organization#Specifics Page \| Result analysis]]
	# [[~~MotiveQuery~~:Specifics Page\| Specifics Page]]		# [[PatternQuery:Specifics Page\| Specifics Page]]
	## [[~~MotiveQuery~~:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[PatternQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[~~MotiveQuery~~:Specifics Page#Fragment Details \| Fragment Details]]		## [[PatternQuery:Specifics Page#Fragment Details \| Fragment Details]]
	## [[~~MotiveQuery~~:Specifics Page#Structure Details \| Structure Details ]]		## [[PatternQuery:Specifics Page#Structure Details \| Structure Details ]]
	----		----

	===[[~~MotiveQuery~~:Language_Reference \| Language reference]]===		===[[PatternQuery:Language_Reference \| Language reference]]===
	----		----
	===[[~~MotiveQuery~~:Command Line \| Command line version & Technical details]]===		===[[PatternQuery:Command Line \| Command line version & Technical details]]===
	----		----

← Older revision		Revision as of 15:40, 20 April 2015
Line 40:		Line 40:
	# [[MotiveQuery:Service Organization#Job Submission \| Job submission]]		# [[MotiveQuery:Service Organization#Job Submission \| Job submission]]
	# [[MotiveQuery:Service Organization#Specifics Page \| Result analysis]]		# [[MotiveQuery:Service Organization#Specifics Page \| Result analysis]]
			# [[MotiveQuery:Specifics Page\| Specifics Page]]
	## [[MotiveQuery:Specifics Page#Calculation Summary\| Calculation Summary]]		## [[MotiveQuery:Specifics Page#Calculation Summary\| Calculation Summary]]
	## [[MotiveQuery:Specifics Page#Fragment Details \| Fragment Details]]		## [[MotiveQuery:Specifics Page#Fragment Details \| Fragment Details]]