Difference between revisions of "Victor"

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The Victor2.0 library ('''Vi'''rtual '''C'''onstruction '''To'''olkit for P'''r'''oteins) is an open-source project dedicated to providing a C++ implementation of tools for analyzing and manipulating protein structures.  
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The Victor library ('''Vi'''rtual '''C'''onstruction '''To'''olkit for P'''r'''oteins) is an open-source project dedicated to providing tools for analyzing and manipulating protein structures. This Wiki will help you to discover how to use the Victor package through an example driven approach. Victor strength is its computational efficiency thanks to a C++ implementation and a vast repertoire of classes and methods. We suggest to read the [[Introduction]] before the [[Tutorial]] to have an overview of the main concepts.
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<br><br>The project is maintained by the '''[http://protein.bio.unipd.it BioComputingUP]''' group.
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<br>The library is distributed under the '''[http://www.gnu.org/licenses/gpl.html GPL license]'''.
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Proteins are particularly suited to machine learning (ML) due to the wealth of available sequence and structural information. This data availability is a result of the recent advances in next generation sequencing technologies and in vitro determination of structures deposited in the Protein Data Bank (PDB). Moreover, nature conserves the same structures and functions thus allowing pattern matching ML approaches to spreadsheet software. However, representing the proteins is a tricky issue, extracting the relevant data became complicated by the protein representations. Thus the first stage of any protein ML approach is complicated by the need to software engineer the data extraction (e.g. extracting residue-residue contacts from a PDB structure). Our lab has recently developed VICTOR which is an easy to use C++ library for extracting relevant protein features. We show that with a simple wrapper VICTOR can be easily incorporated into the ML package WEKA, opening a rich set of ML algorithms to the world of proteins. An interesting example is also shown by clustering the Torsion Angle Potentials (TAPs) of 40,000 protein structures.  
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Victor is composed of three main modules:
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* [[Biopool]] - Biopolymer Object Oriented Library. The core library that generates the protein object and provides useful methods to manipulate the structure.
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* [[Energy]] - Energy functions implementation.
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* [[Lobo]] - LOop Build-up and Optimization.
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This Wiki will help you to discover how to use the Victor package through an example driven approach. We believe this is the easiest way to get confident with the Victor library.
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For a detailed description of all classes and methods please visit the '''Doxygen''' documentation [http://kim.bio.unipd.it/local/DoxyBiopool2014/index.html  Victor2.0 complete guide].
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<div style="background: lightgray; border: 2px; padding: 5px; margin: 10px; border-style: solid; border-color: gray;">
 
[[Getting started]] <hr>Here you will find a resume guide on how to download and install Victor2.0.
 
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[[Detailed Installation]]  <hr>Here you will find a complete guide on how to download and install Victor2.0.
 
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<div style="background: lightgray; border: 2px; padding: 5px; margin: 10px; border-style: solid; border-color: gray;  ">
 
[[Introduction to Victor package]]  <hr>Here you will find an explanation for some of the concepts used for victor2.0 package.
 
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[[Features]] <hr> Here you will find a detailed explanation of the package.
 
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<div class="mainpage_hubtitle"><b>[[Installation]]</b></div>
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<div class="mainpage_boxcontents">
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Getting started. How to '''download''' and '''install''' Victor.
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</div>
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</td>
  
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<td class="mainpage_hubbox" valign="top">
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<div class="mainpage_hubtitle"><b>[[Introduction]]</b></div>
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<div class="mainpage_boxcontents">
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Main concepts and '''theory''' to understand Victor.
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<div class="mainpage_hubtitle"><b>[[Tutorial]]</b></div>
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How to use Victor through a test case '''example'''.
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<td class="mainpage_hubbox" valign="top">
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<div class="mainpage_hubtitle"><b>[[Features]]</b></div>
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'''Cookbook'''. How to use all Victor applications, step-by-step.
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</td>
  
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<div style="background: lightgray; border: 2px; padding: 5px; margin: 10px; border-style: solid; border-color: gray;">
 
[[Tutorial]]  <hr>how to use the Victor package through an example driven approach.
 
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{{Developers}} <hr> Here you will find the detailed documentation for all classes and methods.
 
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[[Community]] <hr> Here you will find information about the research lab Biocomputing Up.
 
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{{References}}  <hr>Here you will find references for some parts of the package.
 
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<div class="mainpage_hubtitle"><b><span class="plainlinks">[[Documentation]]</span></b></div>
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'''Doxygen''' documentation. Detailed description of all classes, methods and '''Unit Test'''.
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<div class="mainpage_hubtitle"><b>[[Community]]</b></div>
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The '''community''' involved in the Victor project.
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{{Applications}}  Here you will find a list of the applications that use the package.
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<td class="mainpage_hubbox" valign="top">
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<div class="mainpage_hubtitle"><b>[[References]]</b></div>
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<div class="mainpage_boxcontents">
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Here you will find '''references''' for some parts of the package.
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</div>
 
</td>
 
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<td class="mainpage_hubbox" valign="top">
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<div class="mainpage_hubtitle"><b>[[Applications]]</b></div>
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<div class="mainpage_boxcontents">
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Here you will find a list of the '''applications''' that use the package.
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</div>
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</td>
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</tr>
 
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Latest revision as of 17:14, 10 October 2014

The Victor library (Virtual Construction Toolkit for Proteins) is an open-source project dedicated to providing tools for analyzing and manipulating protein structures. This Wiki will help you to discover how to use the Victor package through an example driven approach. Victor strength is its computational efficiency thanks to a C++ implementation and a vast repertoire of classes and methods. We suggest to read the Introduction before the Tutorial to have an overview of the main concepts.

The project is maintained by the BioComputingUP group.
The library is distributed under the GPL license.

Getting started. How to download and install Victor.

Main concepts and theory to understand Victor.

How to use Victor through a test case example.

Cookbook. How to use all Victor applications, step-by-step.

Doxygen documentation. Detailed description of all classes, methods and Unit Test.

The community involved in the Victor project.

Here you will find references for some parts of the package.

Here you will find a list of the applications that use the package.