http://wiki.cathdb.info/
2026-03-03T20:22:43+00:00CATH
http://wiki.cathdb.info/
http://wiki.cathdb.info/lib/exe/fetch.php?media=wiki:dokuwiki.svgtext/html2012-09-08T16:15:28+00:00Anonymous (anonymous@undisclosed.example.com)eccb_t2_badasp
http://wiki.cathdb.info/doku.php?id=tutorials:eccb_t2_badasp&rev=1347120928&do=diff
BADASP
BADASP can produce different measures:
* bad: similar the Type II of functional divergence. The threshold to choose depend if we want to be stringeant (i.e. BAD > 4) or more relaxed (BAD > 2).
* badn = BADN variant of BAD: similar the Type Itext/html2012-09-09T09:47:06+00:00Anonymous (anonymous@undisclosed.example.com)eccb_t2_codeml
http://wiki.cathdb.info/doku.php?id=tutorials:eccb_t2_codeml&rev=1347184026&do=diff
CodeML/PAML
Install of PAML
Download it from here: <http://abacus.gene.ucl.ac.uk/software/paml.html#download>
Windows (The bin/ folder already contains windows executables):
cd paml4.6/
Linux:
cd paml4.5/
rm bin/*.exe
cd src
make -f Makefile
ls -l
rm *.o
mv baseml basemlg codeml pamp evolver yn00 chi2 ../bin
chmod +x ../bin/*text/html2012-09-07T16:47:34+00:00Anonymous (anonymous@undisclosed.example.com)eccb_t2_diverge
http://wiki.cathdb.info/doku.php?id=tutorials:eccb_t2_diverge&rev=1347036454&do=diff
Diverge2
There is a self-extracting archive at this website:
<http://xungulab.com/software/diverge2/diverge2.html>
We want to analyse the GAPDH family.
Dowload the following files (alignment and 3D structure), unzip them and load them into Diverge2:
*
*
In the “Clustering” tab, select “text/html2012-09-06T21:10:43+00:00Anonymous (anonymous@undisclosed.example.com)eccb_t2_fundi
http://wiki.cathdb.info/doku.php?id=tutorials:eccb_t2_fundi&rev=1346965843&do=diff
FunDi
Installation
Download it from <https://github.com/dgaston/FunDi>
=> ZIP button
Install it with these commands:
unzip dgaston-FunDi-229c4d6.zip
cd dgaston-FunDi-229c4d6/
unzip qmmraxml.zip
export PATH=$PATH:qmmraxml # Or mv qmmraxml/qmmraxmlHPC to a PATH folder
if not working, you may need to recompile qmmraxmlHPCtext/html2012-09-09T10:31:08+00:00Anonymous (anonymous@undisclosed.example.com)eccb_t2_studer
http://wiki.cathdb.info/doku.php?id=tutorials:eccb_t2_studer&rev=1347186668&do=diff
Practical
Introduction
The presentation is available here:
Useful tools
Jalview: <http://www.jalview.org/download.html>
(It could be better to increase the memory allocated to java: <http://www.jalview.org/jvmmemoryparams.html> )
PyMOL: <http://sourceforge.net/projects/pymol/>
(or <http://sourceforge.net/projects/pymol/files/Legacy/>)
NJplot: <http://pbil.univ-lyon1.fr/software/njplot.html>
Part I on amino acids dataset:
* BADASP: Analysis of the V-type proton ATPase 116 kDa subunit…text/html2012-09-08T16:26:13+00:00Anonymous (anonymous@undisclosed.example.com)eccb_t2_tdg09
http://wiki.cathdb.info/doku.php?id=tutorials:eccb_t2_tdg09&rev=1347121573&do=diff
TDG09
Installation
Download from here:
<http://www.homepages.ucl.ac.uk/~ucbtaut/>
<http://bit.ly/fVbnDr> => tdg09.zip
unzip tdg09.zip
Detection of site in the Influenza Virus Hemagglutinin HA1 chain
We would like to know which sites are important between the Hemagglutinin HA1 of the virus in Avian (genes starting with Av_) and in Human (genes starting with Hu_).text/html2015-09-17T10:48:50+00:00Anonymous (anonymous@undisclosed.example.com)impact_oct_09
http://wiki.cathdb.info/doku.php?id=tutorials:impact_oct_09&rev=1442486930&do=diff
An Introduction to CATH And Gene3D
Welcome to the CATH-Gene3D suite of resources for structural annotation, comparison and prediction.
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Tutorial Map
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A Brief Introductiontext/html2023-09-28T16:20:14+00:00Anonymous (anonymous@undisclosed.example.com)index
http://wiki.cathdb.info/doku.php?id=tutorials:index&rev=1695918014&do=diff
Tutorials
CATH-AlphaFlow ISMB/ECCB 2023 Tutorial
CATH-AlphaFlow is a Nextflow pipeline developed by CATH and the UCL Advanced Research Computing Centre. The pipeline runs various modules of a new version of CATH-Assign, called CATH-AF-CLI. Each module can be ran individually, or as batches via NextFlow.text/html2015-09-21T14:29:47+00:00Anonymous (anonymous@undisclosed.example.com)mali_nov_09
http://wiki.cathdb.info/doku.php?id=tutorials:mali_nov_09&rev=1442845787&do=diff
An Introduction to CATH And Gene3D
Welcome to the CATH-Gene3D suite of resources for structural annotation, comparison and prediction.
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Tutorial Map
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A Brief Introduction
At the heart of the system is the CATH classification of protein domains, derived from integrated semi-automatic processing and manual-curation of high-resolution 3D structures in the wwPDB. From these structures protein domains are identified and co…text/html2015-09-22T14:07:59+00:00Anonymous (anonymous@undisclosed.example.com)mali_tutorial
http://wiki.cathdb.info/doku.php?id=tutorials:mali_tutorial&rev=1442930879&do=diff
Tutorial on CATH and Gene3D
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font-family: Arial, Helvetica, sans-serif;text/html2015-09-21T15:05:16+00:00Anonymous (anonymous@undisclosed.example.com)structural_functional_analysis
http://wiki.cathdb.info/doku.php?id=tutorials:structural_functional_analysis&rev=1442847916&do=diff
CATH Tutorials
Combining Structural and Functional Analysis
<html>
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font-family: Arial, Helvetica, sans-serif;text/html2011-11-16T22:00:10+00:00Anonymous (anonymous@undisclosed.example.com)test
http://wiki.cathdb.info/doku.php?id=tutorials:test&rev=1321480810&do=diff
This is just a test to see if a brand new page can have a discussion box...text/html2012-08-31T13:22:52+00:00Anonymous (anonymous@undisclosed.example.com)testing
http://wiki.cathdb.info/doku.php?id=tutorials:testing&rev=1346419372&do=diff
<jmol :playground:1b86.pdb.gz 400 400>
jmolButton( “cartoon on; cpk off; wireframe off; select *A; color blue; select *B; color red; select *C; color green; select *D; color yellow; select hetero; wireframe on; cpk 50%; color purple; select 6; cartoon off; cpk 60%; color whitetext/html2019-06-19T15:02:13+00:00Anonymous (anonymous@undisclosed.example.com)workshop
http://wiki.cathdb.info/doku.php?id=tutorials:workshop&rev=1560956533&do=diff
Tutorial on CATH and Gene3D
Introduction
In this practical, you will be introduced to the CATH/Gene3D websites and web servers that will help you carry out an investigation into protein structure and function.
<box Info|IMPORTANT NOTES>
This tutorial refers to a number of external websites. It is highly recommended that you click the link with the right-hand mouse button and select either
CATH-Gene3D is a Global Biodata Core Resource Learn more...
CATH-Gene3D is a Global Biodata Core Resource Learn more...