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 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 application. Larger in-house databases can be processed with the 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 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.


Introduction


Terminology

  1. Atom
  2. Residue
  3. Fragment
  4. Query

Principles of the PQ language

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

How to build a query

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

Biological use cases

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

PatternQuery Explorer

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

Using PatternQuery Service

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

Language reference


Command line version & Technical details