NEEMP:UserManual

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).

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Modes

1. Info
2. Cover
3. Charges
4. Cross-validation

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Principles of the PQ language

1. Example - introduction
2. Basic Principle
3. Example - revised

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How to build a query

1. How to think about query
2. Ready-to-use examples

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Biological use cases

1. Post-translational modified aminoacids
2. Zinc fingers
3. Residue containing carbohydrate moiety

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PatternQuery Explorer

1. Launch application
2. How to work with it
3. Execute query

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Using PatternQuery Service

1. Synopsis Page
2. Job submission
3. Specifics Page (result analysis)
   1. Calculation Summary
   2. Pattern Details
   3. Structure Details

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