Editing PatternQuery:UserManual

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'''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: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.
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===[[PatternQuery:Introduction | Introduction]]===
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===[[PatternQuery:Terminology | Terminology]]===
#[[PatternQuery:Terminology#Atom | Atom]]
#[[PatternQuery:Terminology#Residue | Residue]]
#[[PatternQuery:Terminology#Fragment | Fragment]]
#[[PatternQuery:Terminology#Query | Query]]

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===[[PatternQuery:Principles | Principles of the PQ language]]===
#[[PatternQuery:Principles#Example, Part One | Example - introduction]]
#[[PatternQuery:Principles#Basic Principles of the Language | Basic Principle]]
#[[PatternQuery:Principles#Example, Part One | Example - revised]]
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===[[PatternQuery:How to build a query | How to build a query]]===
#[[PatternQuery:How to build a query#How to think about queries | How to think about query]]
#[[PatternQuery:How to build a query#Ready-to-use examples | Ready-to-use examples]]
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===[[PatternQuery:Use Cases | Biological use cases]]===
#[[PatternQuery:Use Cases#Find all post-translational modified amino acids | Post-translational modified aminoacids]]
#[[PatternQuery:Use Cases#Identify Zinc fingers | Zinc fingers]]
#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring | Residue containing carbohydrate moiety]]
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===[[PatternQuery:Explorer | PatternQuery Explorer]]===
# [[PatternQuery:Explorer#Launch PatternQuery Explorer app | Launch application]]
# [[PatternQuery:Explorer#Get started with PatternQuery Explorer | How to work with it]]
# [[PatternQuery:Explorer#Executing Query & interpreting results | Execute query]]
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===[[PatternQuery:Service Organization | Using PatternQuery Service]]===
# [[PatternQuery:Service Organization#Synopsis Page | Synopsis Page]]
# [[PatternQuery:Service Organization#Job Submission | Job submission]]
# [[PatternQuery:Specifics Page| Specifics Page (result analysis)]]
## [[PatternQuery:Specifics Page#Calculation Summary| Calculation Summary]]
## [[PatternQuery:Specifics Page#Pattern Details | Pattern Details]]
## [[PatternQuery:Specifics Page#Structure Details | Structure Details ]]
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===[[PatternQuery:Language_Reference | Language reference]]===
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===[[PatternQuery:Command Line | Command line version & Technical details]]===
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