PatternQuery:Introduction - Revision history

Lukas: /* How can I use it? */

2016-07-21T08:21:07Z

How can I use it?

← Older revision		Revision as of 08:21, 21 July 2016
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	The service is available in 3 different versions:		The service is available in 3 different versions:
	* [[PatternQuery:~~MotiveExplorer~~ \| '''PatternQuery Explorer''']] for querying smaller data sets, or user uploaded data. However, its main advantage lies in perfecting [[PatternQuery:Terminology#Query \| queries]] before one performs PDB-wide searches.		* [[PatternQuery:Explorer \| '''PatternQuery Explorer''']] for querying smaller data sets, or user uploaded data. However, its main advantage lies in perfecting [[PatternQuery:Terminology#Query \| queries]] before one performs PDB-wide searches.
	* [[PatternQuery:Service_Organization\| '''PatternQuery Service''']] - a web HTML/JavaScript interface for the '''PatternQuery Service'''. PDB database or its subset based on a variety of different properties, such as ''Enzymatic number, Organism of Origin'' or ''Resolution'' can be searched using a variety of basic queries.		* [[PatternQuery:Service_Organization\| '''PatternQuery Service''']] - a web HTML/JavaScript interface for the '''PatternQuery Service'''. PDB database or its subset based on a variety of different properties, such as ''Enzymatic number, Organism of Origin'' or ''Resolution'' can be searched using a variety of basic queries.
	* [[PatternQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''PatternQuery''' aimed for querying in house copies of different structural databases.		* [[PatternQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''PatternQuery''' aimed for querying in house copies of different structural databases.

Lukas: /* What is PatternQuery? */

2015-04-25T12:50:05Z

What is PatternQuery?

← Older revision		Revision as of 12:50, 25 April 2015
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	=What is PatternQuery?=		=What is PatternQuery?=

	'''PatternQuery Service''' is an interface to the ''PatternQuery language'' which is simple, yet universal and versatile ~~chemical~~ language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - [http://pdb.org/pdb/home/home.do Protein Data Bank].		'''PatternQuery Service''' is an interface to the ''PatternQuery language'' which is simple, yet universal and versatile atom pattern selection language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - [http://pdb.org/pdb/home/home.do Protein Data Bank].


	=How it can help me?=		=How it can help me?=

Lukas: fragment -> pattern

2015-04-25T12:46:34Z

fragment -> pattern

← Older revision		Revision as of 12:46, 25 April 2015
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	The life sciences, especially namely structural biology, bioinformatics or computational chemistry benefit from the rapid increase of data publicly available. The amount and quality of biomacromolecular sequence and structural data is increasingly growing and the trend won't slow down. This stresses enormous emphasis on the availability of tools for processing and interpreting these data, since deciphering previously unknown features and dependencies sheds more light on a variety of biological processes. Comparative analysis of proteins or their parts helps to uncover their function. Thorough analyses of protein binding schemes inevitably leads for example to the preparation of more stable and versatile catalysts, or helps to find suitable inhibitors of different biological pathways.		The life sciences, especially namely structural biology, bioinformatics or computational chemistry benefit from the rapid increase of data publicly available. The amount and quality of biomacromolecular sequence and structural data is increasingly growing and the trend won't slow down. This stresses enormous emphasis on the availability of tools for processing and interpreting these data, since deciphering previously unknown features and dependencies sheds more light on a variety of biological processes. Comparative analysis of proteins or their parts helps to uncover their function. Thorough analyses of protein binding schemes inevitably leads for example to the preparation of more stable and versatile catalysts, or helps to find suitable inhibitors of different biological pathways.

	=What is ~~MotiveQuery~~?=		=What is PatternQuery?=

	'''~~MotiveQuery~~ Service''' is an interface to the ''~~MotiveQuery~~ language''which is simple, yet universal and versatile chemical language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - [http://pdb.org/pdb/home/home.do Protein Data Bank].		'''PatternQuery Service''' is an interface to the ''PatternQuery language'' which is simple, yet universal and versatile chemical language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - [http://pdb.org/pdb/home/home.do Protein Data Bank].


	=How it can help me?=		=How it can help me?=
	[[File:~~MotiveQuery~~-Intro1.png \| thumb \| 500px \| left\| ''P. aeruginosa '' PA-IIL Lectin (1gzt) sugar binding site identified with '''~~MotiveQuery~~''']]		[[File:PatternQuery-Intro1.png \| thumb \| 500px \| left\| ''P. aeruginosa '' PA-IIL Lectin (1gzt) sugar binding site identified with '''PatternQuery''']]

	'''~~MotiveQuery~~''' is tailored to describe biomacromolecular structural [[~~MotiveQuery~~:Terminology#~~Fragment~~ \| ~~fragments~~]] based on the nature and the relationship between [[~~MotiveQuery~~:Terminology#Atom \| atoms]], [[~~MotiveQuery~~:Terminology#Residue \| residues]], and other structural elements, both at the sequence and 3D level. This unique design allows the user to simultaneously operate and combine several levels of resolution to identify ~~fragments~~ of biomacromolecular complexes including ligands, water molecules, and ions. Such knowledge has a variety of imminent applications, for example: 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''' is tailored to describe biomacromolecular structural [[PatternQuery:Terminology#Pattern \| patterns]] based on the nature and the relationship between [[PatternQuery:Terminology#Atom \| atoms]], [[PatternQuery:Terminology#Residue \| residues]], and other structural elements, both at the sequence and 3D level. This unique design allows the user to simultaneously operate and combine several levels of resolution to identify patterns of biomacromolecular complexes including ligands, water molecules, and ions. Such knowledge has a variety of imminent applications, for example: 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.
	<br style="clear:both" />		<br style="clear:both" />

	=How can I use it?=		=How can I use it?=

	[[File:~~MotiveQuery~~-Intro2.png \| thumb \|500px \| right \| Example of query identifying testosterone binding site '''~~MotiveQuery~~''']]		[[File:PatternQuery-Intro2.png \| thumb \|500px \| right \| Example of query identifying testosterone binding site '''PatternQuery''']]

	The service is available in 3 different versions:		The service is available in 3 different versions:
	* [[~~MotiveQuery~~:MotiveExplorer \| '''~~MotiveQuery~~ Explorer''']] for querying smaller data sets, or user uploaded data. However, its main advantage lies in perfecting [[~~MotiveQuery~~:Terminology#Query \| queries]] before one performs PDB-wide searches.		* [[PatternQuery:MotiveExplorer \| '''PatternQuery Explorer''']] for querying smaller data sets, or user uploaded data. However, its main advantage lies in perfecting [[PatternQuery:Terminology#Query \| queries]] before one performs PDB-wide searches.
	* [[~~MotiveQuery~~:Service_Organization\| '''~~MotiveQuery~~ Service''']] - a web HTML/JavaScript interface for the '''~~MotiveQuery~~ Service'''. PDB database or its subset based on a variety of different properties, such as ''Enzymatic number, Organism of Origin'' or ''Resolution'' can be searched using a variety of basic queries.		* [[PatternQuery:Service_Organization\| '''PatternQuery Service''']] - a web HTML/JavaScript interface for the '''PatternQuery Service'''. PDB database or its subset based on a variety of different properties, such as ''Enzymatic number, Organism of Origin'' or ''Resolution'' can be searched using a variety of basic queries.
	* [[~~MotiveQuery~~:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''~~MotiveQuery~~''' aimed for querying in house copies of different structural databases.		* [[PatternQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''PatternQuery''' aimed for querying in house copies of different structural databases.

	For further information on how to control the application please take a look at the relevant wiki pages, or directly use the [http://webchem.ncbr.muni.cz/Platform/~~MotiveQuery~~/Index application]. Whenever you are unsure on how to carry on, use one of the many guides (reachable by ''?'' button) which are there for your convenience. If you need additional help, contact information is directly included in the '''Support tab''' on the [http://webchem.ncbr.muni.cz/Platform/~~MotiveQuery~~/Index#support-tab\| web].		For further information on how to control the application please take a look at the relevant wiki pages, or directly use the [http://webchem.ncbr.muni.cz/Platform/PatternQuery/Index application]. Whenever you are unsure on how to carry on, use one of the many guides (reachable by ''?'' button) which are there for your convenience. If you need additional help, contact information is directly included in the '''Support tab''' on the [http://webchem.ncbr.muni.cz/Platform/PatternQuery/Index#support-tab\| web].
	<br style="clear:both" />		<br style="clear:both" />

	=Where should I start?=		=Where should I start?=

	Before you write your first query, it is many times useful to go through our manual, on [[~~MotiveQuery~~:How to build a query \| how to write a query]] or take a look into the [[~~MotiveQuery~~:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''~~MotiveQuery~~''' interface for your convenience. If neither of them helps, ''Ask us'' a question via a simple [http://webchem.ncbr.muni.cz/Platform/~~MotiveQuery~~/Index#support-tab\| user interface]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.		Before you write your first query, it is many times useful to go through our manual, on [[PatternQuery:How to build a query \| how to write a query]] or take a look into the [[PatternQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''PatternQuery''' interface for your convenience. If neither of them helps, ''Ask us'' a question via a simple [http://webchem.ncbr.muni.cz/Platform/PatternQuery/Index#support-tab\| user interface]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.

	'''Enjoy working with ~~MotiveQuery~~!'''		'''Enjoy working with PatternQuery!'''

Lukas: Lukas moved page MotiveQuery:Introduction to PatternQuery:Introduction: Service name change

2015-04-25T12:44:33Z

Lukas moved page MotiveQuery:Introduction to PatternQuery:Introduction: Service name change

← Older revision	Revision as of 12:44, 25 April 2015
(No difference)

Lukas at 14:21, 20 April 2015

2015-04-20T14:21:35Z

← Older revision		Revision as of 14:21, 20 April 2015
Line 1:		Line 1:
	__NOTOC__		__NOTOC__

	~~All the~~ life sciences, namely structural biology, bioinformatics or computational chemistry ~~benefits~~ from the rapid increase of data publicly available. The amount and quality of biomacromolecular sequence and structural data ~~were~~ increasingly growing ~~in the past decade~~ and ~~it seems that~~ the trend ~~isn~~'t to slow down ~~any time soon~~. This stresses enormous emphasis on the availability of tools for processing and interpreting these data, since deciphering previously unknown features and dependencies sheds more light on a variety of biological processes. Comparative analysis of proteins or ~~its~~ parts helps to uncover their function. Thorough analyses of protein binding schemes inevitably leads for example to the preparation of more stable and versatile ~~catalysis~~, or helps to find suitable inhibitors of different biological pathways.		The life sciences, especially namely structural biology, bioinformatics or computational chemistry benefit from the rapid increase of data publicly available. The amount and quality of biomacromolecular sequence and structural data is increasingly growing and the trend won't slow down. This stresses enormous emphasis on the availability of tools for processing and interpreting these data, since deciphering previously unknown features and dependencies sheds more light on a variety of biological processes. Comparative analysis of proteins or their parts helps to uncover their function. Thorough analyses of protein binding schemes inevitably leads for example to the preparation of more stable and versatile catalysts, or helps to find suitable inhibitors of different biological pathways.

	=What is MotiveQuery?=		=What is MotiveQuery?=

	'''MotiveQuery Service''' is an interface to the ''MotiveQuery language'' simple, yet universal and versatile chemical language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - [http://pdb.org/pdb/home/home.do Protein Data Bank].		'''MotiveQuery Service''' is an interface to the ''MotiveQuery language''which is simple, yet universal and versatile chemical language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - [http://pdb.org/pdb/home/home.do Protein Data Bank].


Line 11:		Line 11:
	[[File:MotiveQuery-Intro1.png \| thumb \| 500px \| left\| ''P. aeruginosa '' PA-IIL Lectin (1gzt) sugar binding site identified with '''MotiveQuery''']]		[[File:MotiveQuery-Intro1.png \| thumb \| 500px \| left\| ''P. aeruginosa '' PA-IIL Lectin (1gzt) sugar binding site identified with '''MotiveQuery''']]

	'''MotiveQuery''' is tailored to describe biomacromolecular structural [[MotiveQuery:Terminology#Fragment \| fragments]] based on the nature and the relationship between [[MotiveQuery:Terminology#Atom \| atoms]], [[MotiveQuery:Terminology#Residue \| residues]], and other structural elements, both at the sequence and 3D level. This unique design allows the user to simultaneously operate and combine several levels of resolution to identify fragments of biomacromolecular complexes including ligands, water molecules, and ions. Such knowledge ~~have~~ a variety of imminent applications, for example: 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''' is tailored to describe biomacromolecular structural [[MotiveQuery:Terminology#Fragment \| fragments]] based on the nature and the relationship between [[MotiveQuery:Terminology#Atom \| atoms]], [[MotiveQuery:Terminology#Residue \| residues]], and other structural elements, both at the sequence and 3D level. This unique design allows the user to simultaneously operate and combine several levels of resolution to identify fragments of biomacromolecular complexes including ligands, water molecules, and ions. Such knowledge has a variety of imminent applications, for example: 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.
	<br style="clear:both" />		<br style="clear:both" />

Line 19:		Line 19:

	The service is available in 3 different versions:		The service is available in 3 different versions:
	* [[MotiveQuery:MotiveExplorer \| '''MotiveQuery Explorer''']] for querying smaller data sets, or user uploaded data. However its main advantage lies in perfecting [[MotiveQuery:Terminology#Query \| queries]] before one performs PDB-wide searches.		* [[MotiveQuery:MotiveExplorer \| '''MotiveQuery Explorer''']] for querying smaller data sets, or user uploaded data. However, its main advantage lies in perfecting [[MotiveQuery:Terminology#Query \| queries]] before one performs PDB-wide searches.
	* [[MotiveQuery:Service_Organization\| '''MotiveQuery Service''']] - a web HTML/JavaScript interface for the '''MotiveQuery Service'''. PDB database or its subset based on a variety of different properties, such as ''Enzymatic number, Organism of Origin'' or ''Resolution''.		* [[MotiveQuery:Service_Organization\| '''MotiveQuery Service''']] - a web HTML/JavaScript interface for the '''MotiveQuery Service'''. PDB database or its subset based on a variety of different properties, such as ''Enzymatic number, Organism of Origin'' or ''Resolution'' can be searched using a variety of basic queries.
	* [[MotiveQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''MotiveQuery''' aimed for querying in house copies of different structural databases.		* [[MotiveQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''MotiveQuery''' aimed for querying in house copies of different structural databases.

	For further information on how to control the application please take a look at the relevant wiki pages, or directly use the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index application]. Whenever you are unsure on how to carry on, use one of the many guides (reachable by ''?'' button) which are there for your convenience.		For further information on how to control the application please take a look at the relevant wiki pages, or directly use the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index application]. Whenever you are unsure on how to carry on, use one of the many guides (reachable by ''?'' button) which are there for your convenience. If you need additional help, contact information is directly included in the '''Support tab''' on the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| web].
	<br style="clear:both" />		<br style="clear:both" />

Lukas: /* Where should I start? */

2014-12-28T20:20:47Z

Where should I start?

← Older revision		Revision as of 20:20, 28 December 2014
Line 28:		Line 28:
	=Where should I start?=		=Where should I start?=

	Before you write your first query, it is many times useful to go through our manual, on [[MotiveQuery:How to build a query \| how to write a query]] or take a look into the [[MotiveQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''MotiveQuery''' interface for your convenience. If neither of them helps, ''Ask us'' a question via a simple [[http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| user interface]]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.		Before you write your first query, it is many times useful to go through our manual, on [[MotiveQuery:How to build a query \| how to write a query]] or take a look into the [[MotiveQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''MotiveQuery''' interface for your convenience. If neither of them helps, ''Ask us'' a question via a simple [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| user interface]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.

	'''Enjoy working with MotiveQuery!'''		'''Enjoy working with MotiveQuery!'''

Lukas: /* Where should I start? */

2014-12-28T20:20:28Z

Where should I start?

← Older revision		Revision as of 20:20, 28 December 2014
Line 30:		Line 30:
	Before you write your first query, it is many times useful to go through our manual, on [[MotiveQuery:How to build a query \| how to write a query]] or take a look into the [[MotiveQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''MotiveQuery''' interface for your convenience. If neither of them helps, ''Ask us'' a question via a simple [[http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| user interface]]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.		Before you write your first query, it is many times useful to go through our manual, on [[MotiveQuery:How to build a query \| how to write a query]] or take a look into the [[MotiveQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''MotiveQuery''' interface for your convenience. If neither of them helps, ''Ask us'' a question via a simple [[http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| user interface]]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.

	'''Enjoy working with MotiveQuery'''		'''Enjoy working with MotiveQuery!'''

Lukas: /* Where should I start? */

2014-12-28T19:27:34Z

Where should I start?

← Older revision		Revision as of 19:27, 28 December 2014
Line 28:		Line 28:
	=Where should I start?=		=Where should I start?=

	Before you write your first query, it is many times useful to go through our manual, on [[MotiveQuery:How to build a query \| how to write a query]] or take a look into the [[MotiveQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''MotiveQuery''' interface for your ~~convenient~~. If neither of them helps, Ask us a question via a simple [[http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| user interface]]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.		Before you write your first query, it is many times useful to go through our manual, on [[MotiveQuery:How to build a query \| how to write a query]] or take a look into the [[MotiveQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''MotiveQuery''' interface for your convenience. If neither of them helps, ''Ask us'' a question via a simple [[http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| user interface]]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.

	'''Enjoy working with MotiveQuery'''		'''Enjoy working with MotiveQuery'''

Lukas: /* How can I use it? */

2014-12-28T19:26:26Z

How can I use it?

← Older revision		Revision as of 19:26, 28 December 2014
Line 23:		Line 23:
	* [[MotiveQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''MotiveQuery''' aimed for querying in house copies of different structural databases.		* [[MotiveQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''MotiveQuery''' aimed for querying in house copies of different structural databases.

	For further information on how to control the application please take a look at the relevant wiki pages, or directly use the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index application].		For further information on how to control the application please take a look at the relevant wiki pages, or directly use the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index application]. Whenever you are unsure on how to carry on, use one of the many guides (reachable by ''?'' button) which are there for your convenience.
	<br style="clear:both" />		<br style="clear:both" />

Lukas: Initial commit

2014-12-28T19:22:36Z

Initial commit

← Older revision	Revision as of 19:22, 28 December 2014
Line 1:	Line 1:
		__NOTOC__

		All the life sciences, namely structural biology, bioinformatics or computational chemistry benefits from the rapid increase of data publicly available. The amount and quality of biomacromolecular sequence and structural data were increasingly growing in the past decade and it seems that the trend isn't to slow down any time soon. This stresses enormous emphasis on the availability of tools for processing and interpreting these data, since deciphering previously unknown features and dependencies sheds more light on a variety of biological processes. Comparative analysis of proteins or its parts helps to uncover their function. Thorough analyses of protein binding schemes inevitably leads for example to the preparation of more stable and versatile catalysis, or helps to find suitable inhibitors of different biological pathways.

		=What is MotiveQuery?=

		'''MotiveQuery Service''' is an interface to the ''MotiveQuery language'' simple, yet universal and versatile chemical language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - [http://pdb.org/pdb/home/home.do Protein Data Bank].


		=How it can help me?=
		[[File:MotiveQuery-Intro1.png \| thumb \| 500px \| left\| ''P. aeruginosa '' PA-IIL Lectin (1gzt) sugar binding site identified with '''MotiveQuery''']]

		'''MotiveQuery''' is tailored to describe biomacromolecular structural [[MotiveQuery:Terminology#Fragment \| fragments]] based on the nature and the relationship between [[MotiveQuery:Terminology#Atom \| atoms]], [[MotiveQuery:Terminology#Residue \| residues]], and other structural elements, both at the sequence and 3D level. This unique design allows the user to simultaneously operate and combine several levels of resolution to identify fragments of biomacromolecular complexes including ligands, water molecules, and ions. Such knowledge have a variety of imminent applications, for example: 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.
		<br style="clear:both" />

		=How can I use it?=

		[[File:MotiveQuery-Intro2.png \| thumb \|500px \| right \| Example of query identifying testosterone binding site '''MotiveQuery''']]

		The service is available in 3 different versions:
		* [[MotiveQuery:MotiveExplorer \| '''MotiveQuery Explorer''']] for querying smaller data sets, or user uploaded data. However its main advantage lies in perfecting [[MotiveQuery:Terminology#Query \| queries]] before one performs PDB-wide searches.
		* [[MotiveQuery:Service_Organization\| '''MotiveQuery Service''']] - a web HTML/JavaScript interface for the '''MotiveQuery Service'''. PDB database or its subset based on a variety of different properties, such as ''Enzymatic number, Organism of Origin'' or ''Resolution''.
		* [[MotiveQuery:Command_Line#Running the Offline Service \| '''Command-line application''']] an offline version of '''MotiveQuery''' aimed for querying in house copies of different structural databases.

		For further information on how to control the application please take a look at the relevant wiki pages, or directly use the [http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index application].
		<br style="clear:both" />

		=Where should I start?=

		Before you write your first query, it is many times useful to go through our manual, on [[MotiveQuery:How to build a query \| how to write a query]] or take a look into the [[MotiveQuery:Language Reference \| language reference]]. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at '''MotiveQuery''' interface for your convenient. If neither of them helps, Ask us a question via a simple [[http://webchem.ncbr.muni.cz/Platform/MotiveQuery/Index#support-tab\| user interface]]. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.

		'''Enjoy working with MotiveQuery'''