Difference between revisions of "PICv"

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{{Infobox script-repo
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|type = plugin
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|download = [http://vidyaniranjan.co.in/PICv/PICv.py '''PICv''']
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|author = [https://akshayuttarkar.wixsite.com/akshay Akshay Uttarkar], [https://vpdesai2020.github.io/vasanth.github.io/  Vasanth Kumar Desai], Namitha P, John Berrisford, [https://www.ebi.ac.uk/about/people/sameer-velankar Sameer Velankar], [http://www.vidyaniranjan.co.in/ Vidya Niranjan]* 
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|license = GNU Free Documentation License 1.2
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}}
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== '''About PICv''' ==
 
== '''About PICv''' ==
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[[File:PICv.png]]
 
[[File:PICv.png]]
  
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Protein interaction clustering and visualization (PICv) is a pioneering attempt at clustering and understanding protein-protein interaction for any given protein by implementing ML based clustering. The PyMOL plugin facilitates importing of the best PDB structure for a given protein and 3D-visualization of protein-protein interaction interface clusters.
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Protein interaction clustering and visualization is an pioneer attempt in understanding protein-protein interaction at a residue level. For any given protein the interaction is purely dependent on its charges and surface-structural modifications. The clustering of proteins based on there preferential amino acid interactions provides a biological insight on both the above mentioned aspects. The clusters such obtained can be used to infer the interaction behavior for a class or family of proteins. Such interpretation can be useful in understanding structural protein chemistry. The interactions also provide information on the crucial amino acids required for interactions to remain stable. This information can be used to design antibody or induce mutations to depreciate its functionality
  
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[[File:PICv_home_screen.PNG]]
  
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== '''Installation''' ==
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== '''Code''' ==
 
Download the plugin from the following URL:
 
Download the plugin from the following URL:
  
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http://vidyaniranjan.co.in/PICv/PICv.py
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[http://vidyaniranjan.co.in/PICv/PICv.py '''PICv Source Code''']
  
 
== '''Installation and Demo video''' ==
 
== '''Installation and Demo video''' ==
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Visit the below mentioned link for detailed installation followed by demo.
 
Visit the below mentioned link for detailed installation followed by demo.
  
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https://youtu.be/3bxpASy-FV0
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[https://youtu.be/3bxpASy-FV0 '''PICv (Video)''']
  
 
== '''Developed by''' ==
 
== '''Developed by''' ==
  
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The plugin was developed by Center of Excellence Computational Genomics, R V College of Engineering, Bangalore, India in collaboration with Protein Data Bank in Europe (PDBe), UK
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The plugin was developed by '''Center of Excellence Computational Genomics''', R V College of Engineering, Bangalore, India in collaboration with '''Protein Data Bank in Europe (PDBe), UK'''
  
 
'''For more details visit'''
 
'''For more details visit'''
  
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http://www.vidyaniranjan.co.in/
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[http://www.vidyaniranjan.co.in/ '''Center of Excellence Computational Genomics''']
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== '''Copyright''' ==
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<source lang="text">
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# Copyright Notice
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# ================
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#
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# The PyMOL Plugin source code in this file is copyrighted, but you are
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# free to use and copy it as long as you don't change or remove any of
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# the copyright notices.
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#
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# -----------------------------------------------------------------------------------
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# This PyMOL Plugin PICv is
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# Copyright (C) 2021 by Vidya Niranjan <vidya.n@rvce.edu.in>
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#
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#                        All Rights Reserved
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#
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# Permission to use, copy, modify, distribute, and distribute modified
 +
# versions of this software and its documentation for any purpose and
 +
# without fee is hereby granted, provided that the above copyright
 +
# notice appear in all copies and that both the copyright notice and
 +
# this permission notice appear in supporting documentation, and that
 +
# the name(s) of the author(s) not be used in advertising or publicity
 +
# pertaining to distribution of the software without specific, written
 +
# prior permission.
 +
#
 +
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
 +
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.  IN
 +
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR
 +
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
 +
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
 +
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
 +
# PERFORMANCE OF THIS SOFTWARE.
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#
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</source>
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[[Category:Plugins]]
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[[Category:Pymol-script-repo]]

Latest revision as of 07:17, 26 July 2021

Type PyMOL Plugin
Download PICv
Author(s) Akshay Uttarkar, Vasanth Kumar Desai, Namitha P, John Berrisford, Sameer Velankar, Vidya Niranjan*
License GNU Free Documentation License 1.2




About PICv

PICv.png

Protein interaction clustering and visualization is an pioneer attempt in understanding protein-protein interaction at a residue level. For any given protein the interaction is purely dependent on its charges and surface-structural modifications. The clustering of proteins based on there preferential amino acid interactions provides a biological insight on both the above mentioned aspects. The clusters such obtained can be used to infer the interaction behavior for a class or family of proteins. Such interpretation can be useful in understanding structural protein chemistry. The interactions also provide information on the crucial amino acids required for interactions to remain stable. This information can be used to design antibody or induce mutations to depreciate its functionality

PICv home screen.PNG

Code

Download the plugin from the following URL:

PICv Source Code

Installation and Demo video

Visit the below mentioned link for detailed installation followed by demo.

PICv (Video)

Developed by

The plugin was developed by Center of Excellence Computational Genomics, R V College of Engineering, Bangalore, India in collaboration with Protein Data Bank in Europe (PDBe), UK

For more details visit

Center of Excellence Computational Genomics

Copyright

# Copyright Notice
# ================
# 
# The PyMOL Plugin source code in this file is copyrighted, but you are
# free to use and copy it as long as you don't change or remove any of
# the copyright notices.
# 
# -----------------------------------------------------------------------------------
# This PyMOL Plugin PICv is
# Copyright (C) 2021 by Vidya Niranjan <vidya.n@rvce.edu.in>
# 
#                        All Rights Reserved
# 
# Permission to use, copy, modify, distribute, and distribute modified
# versions of this software and its documentation for any purpose and
# without fee is hereby granted, provided that the above copyright
# notice appear in all copies and that both the copyright notice and
# this permission notice appear in supporting documentation, and that
# the name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
# 
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.  IN
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
# PERFORMANCE OF THIS SOFTWARE.
#
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