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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. | | '''NEEMP''' is the first freely available software for EEM parametrization, EEM charges validation and EEM charges calculation. |
| | This Wiki page is intended to guide the user through '''NEEMP''' functionalities, providing complete but simple descriptions of the software features and helpful examples on its usage. |
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| '''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]].
| | For a more detailed and thorough description of '''NEEMP''''s methods and implementation we refer the user to the links at the bottom of this page ([[NEEMP:References | References]]). |
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| 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]]=== | | ===[[PatternQuery:Introduction | Introduction]]=== |
NEEMP is the first freely available software for EEM parametrization, EEM charges validation and EEM charges calculation.
This Wiki page is intended to guide the user through NEEMP functionalities, providing complete but simple descriptions of the software features and helpful examples on its usage.
For a more detailed and thorough description of NEEMP's methods and implementation we refer the user to the links at the bottom of this page ( References).
- Atom
- Residue
- Fragment
- Query
- Example - introduction
- Basic Principle
- Example - revised
- How to think about query
- Ready-to-use examples
- Post-translational modified aminoacids
- Zinc fingers
- Residue containing carbohydrate moiety
- Launch application
- How to work with it
- Execute query
- Synopsis Page
- Job submission
- Specifics Page (result analysis)
- Calculation Summary
- Pattern Details
- Structure Details