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| ---- | | ---- |
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| ===[[PatternQuery:How to build a query | How to build a query]]=== | | ===[[NEEMP:files | Used file formats]]=== |
| #[[PatternQuery:How to build a query#How to think about queries | How to think about query]] | | #[[NEEMP:files#SDF file | SDF file]] |
| #[[PatternQuery:How to build a query#Ready-to-use examples | Ready-to-use examples]] | | #[[NEEMP:files#CHG file | CHG file]] |
| | #[[NEEMP:files#PAR file | PAR file]] |
| ---- | | ---- |
| ===[[PatternQuery:Use Cases | Biological use cases]]=== | | ===[[NEEMP:Examples | Examples]]=== |
| #[[PatternQuery:Use Cases#Find all post-translational modified amino acids | Post-translational modified aminoacids]] | | #[[NEEMP:Examples#Example 1 | Example 1]] |
| #[[PatternQuery:Use Cases#Identify Zinc fingers | Zinc fingers]] | | #[[NEEMP:Examples#Example 2 | Example 2]] |
| #[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring | Residue containing carbohydrate moiety]] | | #[[NEEMP:Examples#Example 3 | Example 3]] |
| | #[[NEEMP:Examples#Example 4 | Example 4]] |
| | #[[NEEMP:Examples#Example 5 | Example 5]] |
| | #[[NEEMP:Examples#Example 6 | Example 6]] |
| | #[[NEEMP:Examples#Example 7 | Example 7]] |
| | #[[NEEMP:Examples#Example 8 | Example 8]] |
| | #[[NEEMP:Examples#Example 9 | Example 9]] |
| ---- | | ---- |
| ===[[PatternQuery:Explorer | PatternQuery Explorer]]=== | | ===[[NEEMP:References | References]]=== |
| # [[PatternQuery:Explorer#Launch PatternQuery Explorer app | Launch application]]
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| # [[PatternQuery:Explorer#Get started with PatternQuery Explorer | How to work with it]]
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| # [[PatternQuery:Explorer#Executing Query & interpreting results | Execute query]]
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| ----
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| ===[[PatternQuery:Service Organization | Using PatternQuery Service]]===
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| # [[PatternQuery:Service Organization#Synopsis Page | Synopsis Page]]
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| # [[PatternQuery:Service Organization#Job Submission | Job submission]]
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| # [[PatternQuery:Specifics Page| Specifics Page (result analysis)]]
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| ## [[PatternQuery:Specifics Page#Calculation Summary| Calculation Summary]]
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| ## [[PatternQuery:Specifics Page#Pattern Details | Pattern Details]]
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| ## [[PatternQuery:Specifics Page#Structure Details | Structure Details ]]
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| ----
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| ===[[PatternQuery:Language_Reference | Language reference]]===
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| ----
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| ===[[PatternQuery:Command Line | Command line version & Technical details]]===
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| ---- | | ---- |
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).
- Info
- Cover
- Charges
- Cross-validation
- k settings
- Discarding
- Simple discarding
- Iterative discarding
- Other options
- Miscellaneous
- Parallelism
- Statistics computation
- SDF file
- CHG file
- PAR file
- Example 1
- Example 2
- Example 3
- Example 4
- Example 5
- Example 6
- Example 7
- Example 8
- Example 9