I have some deduced sequences for a specific protein from diseased as well as apparently healthy animals, I just want to detect active sites and see differences and their effect if any.
COACH is currently ranked as the best method in the ongoing CAMEO ligand binding experiment for assessing how well function prediction programs are doing.
description of the method
http://zhanglab.ccmb.med.umich.edu/COACH/COACH.pdf
performance in cameo experiment
http://www.cameo3d.org/lb/1-year/
example results
http://zhanglab.ccmb.med.umich.edu/COACH/CH000001/
Note: COACH uses as a structure as an input. The standard algorithim is to run the sequence through ITASSER first to model the structure and then use COACH to determine the binding site.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
ITASSER by default will run another function prediction program COFACTOR.
example of cofactor results
http://zhanglab.ccmb.med.umich.edu/COFACTOR/example/
Some other programs can be found in the link below
http://onlinelibrary.wiley.com/doi/10.1002/prot.24495/abstract
Dr. Brender,
thanks for the useful reply.
i had noticed that the single job in COACH takes about 10 hours.
isn't it a long time?
how many sequences do you have?
Most of the time is spent in modelling the structure. Although structure based detection is more accurate then sequence based (see the link above) if you have hundreds of sequences it may not be practical. However, if the sequences represent SNPs or other minor variants of a parent sequences it should be possible to speed this up considerably.
i had received several errors with my first job, the i cant view my result (error.click for detail)
when i had clicked i found this report.
my system is windows 8.1
Java Plug-in 10.55.2.14
Using JRE version 1.7.0_55-b14 Java HotSpot(TM) Client VM
User home directory = C:\Users\Dr.Basem
----------------------------------------------------
c: clear console window
f: finalize objects on finalization queue
g: garbage collect
h: display this help message
l: dump classloader list
m: print memory usage
o: trigger logging
q: hide console
r: reload policy configuration
s: dump system and deployment properties
t: dump thread list
v: dump thread stack
x: clear classloader cache
0-5: set trace level to
----------------------------------------------------
java.lang.NullPointerException
at sun.awt.SunToolkit.getSystemEventQueueImplPP(Unknown Source)
at sun.awt.SunToolkit.getSystemEventQueueImplPP(Unknown Source)
at sun.awt.SunToolkit.getSystemEventQueueImpl(Unknown Source)
at java.awt.Toolkit.getEventQueue(Unknown Source)
at java.awt.EventQueue.invokeLater(Unknown Source)
at sun.awt.windows.WToolkit.windowsSettingChange(Unknown Source)
at sun.awt.windows.WToolkit.eventLoop(Native Method)
at sun.awt.windows.WToolkit.run(Unknown Source)
the Zhang lab servers are running a different version of JRE which can cause some problems.
1. Can you open up this page
http://zhanglab.ccmb.med.umich.edu/COACH/CH000001/
and see if you can see the result?
2. Can you send me the job ID by message or email ( [email protected]) so I can take a look at your result? I have direct access to the servers and code.
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