PatternQuery:Introduction

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The life sciences, especially namely structural biology, bioinformatics or computational chemistry benefit from the rapid increase of data publicly available. The amount and quality of biomacromolecular sequence and structural data is increasingly growing and the trend won't slow down. This stresses enormous emphasis on the availability of tools for processing and interpreting these data, since deciphering previously unknown features and dependencies sheds more light on a variety of biological processes. Comparative analysis of proteins or their parts helps to uncover their function. Thorough analyses of protein binding schemes inevitably leads for example to the preparation of more stable and versatile catalysts, or helps to find suitable inhibitors of different biological pathways.

What is PatternQuery?

PatternQuery Service is an interface to the PatternQuery language which is simple, yet universal and versatile atom pattern selection language. The language allows you to perform a variety of searches - from simple identification of ions or ligands and their binding sites, through detection of specific binding motifs such as zinc-fingers, to complex pharmacophores modulating biological activity. These searches are performed over the largest database of biomacromolecular structures - Protein Data Bank.

How it can help me?

P. aeruginosa PA-IIL Lectin (1gzt) sugar binding site identified with PatternQuery

PatternQuery is tailored to describe biomacromolecular structural patterns based on the nature and the relationship between atoms, residues, and other structural elements, both at the sequence and 3D level. This unique design allows the user to simultaneously operate and combine several levels of resolution to identify patterns of biomacromolecular complexes including ligands, water molecules, and ions. Such knowledge has a variety of imminent applications, for example: 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.

How can I use it?

Example of query identifying testosterone binding site PatternQuery

The service is available in 3 different versions:

  • PatternQuery Explorer for querying smaller data sets, or user uploaded data. However, its main advantage lies in perfecting queries before one performs PDB-wide searches.
  • PatternQuery Service - a web HTML/JavaScript interface for the PatternQuery Service. PDB database or its subset based on a variety of different properties, such as Enzymatic number, Organism of Origin or Resolution can be searched using a variety of basic queries.
  • Command-line application an offline version of PatternQuery aimed for querying in house copies of different structural databases.

For further information on how to control the application please take a look at the relevant wiki pages, or directly use the application. Whenever you are unsure on how to carry on, use one of the many guides (reachable by ? button) which are there for your convenience. If you need additional help, contact information is directly included in the Support tab on the web.

Where should I start?

Before you write your first query, it is many times useful to go through our manual, on how to write a query or take a look into the language reference. If you do not feel like reading anything, you can try and browse one of our ready-to-use samples or examples, which are ready at PatternQuery interface for your convenience. If neither of them helps, Ask us a question via a simple user interface. We will do our best to get back to you as soon as possible. We are always happy to answer your questions related to the service, or even to help you constructing your queries for your own research.

Enjoy working with PatternQuery!