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.

Your computer is blocking the older version of Java the Zhang lab servers are running

Solution

1. Go to the Java then Configure Java and then the Security Tab

2. Click Edit site list

3. Paste http://zhanglab.ccmb.med.umich.edu/ into the box and then click add

4. When the page is loaded next time it will ask if you want to run an untrusted applet from this site. Click "yes" and it will run normally.

This works for all Zhang lab server programs