Proteopedia - User contributions [en]

User:Nir London/FunHunt

2008-09-18T11:46:14Z

Nir London:

<applet load='1STF_2.pdb' size='300' frame='true' align='right' caption='Insert caption here' name='2'/>
<applet load='1STF_1.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are two docking models for the complex of recombinant human Stefin B with cysteine proteinase Papain. One of the models is correct while the other is incorrect, can you tell which is which ? <scene name='User:Nir_London/FunHunt/1stf_correct/1'>Click here</scene> to color the correct model blue and find out if you were correct. Let's try this: color the second one <scene name='User:Nir_London/FunHunt/1stp_2_blue/1' target='2'>blue</scene>.

==FunHunt==
FunHunt <ref>London N., Schueler-Furman O. (2008) Funnel hunting in a rough terrain: learning and discriminating native energy funnels. Structure. 16:269-79. </ref><ref>London N., Schueler-Furman O. (2007) Assessing the energy landscape of CAPRI targets by FunHunt. Proteins. 69:809-15</ref> is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).
FunHunt is available via the web. Try it! [http://funhunt.furmanlab.cs.huji.ac.il].

==References==

<references/>

User:Nir London/FunHunt

2008-09-18T11:41:31Z

Nir London:

<applet load='1STF_2.pdb' size='300' frame='true' align='right' caption='Insert caption here' name='2'/>
<applet load='1STF_1.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are two docking models for the complex of recombinant human Stefin B with cysteine proteinase Papain. One of the models is correct while the other is incorrect, can you tell which is which ? <scene name='User:Nir_London/FunHunt/1stf_correct/1'>Click here</scene> to color the correct model blue and find out if you were correct. Let's try this: color the second one <scene name='User:Nir_London/FunHunt/1stp_2_blue/1' target='2'>blue</scene>.

==FunHunt==
FunHunt <ref>London N., Schueler-Furman O. (2008) Funnel hunting in a rough terrain: learning and discriminating native energy funnels. Structure. 16:269-79. </ref><ref>London N., Schueler-Furman O. (2007) Assessing the energy landscape of CAPRI targets by FunHunt. Proteins. 69:809-15</ref>is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==References==

<references/>

User:Nir London/FunHunt

2008-09-18T11:31:57Z

Nir London:

<applet load='1STF_2.pdb' size='300' frame='true' align='right' caption='Insert caption here' name='2'/>
<applet load='1STF_1.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are two docking models for the complex of recombinant human Stefin B with cysteine proteinase Papain. One of the models is correct while the other is incorrect, can you tell which is which ? <scene name='User:Nir_London/FunHunt/1stf_correct/1'>Click here</scene> to color the correct model blue and find out if you were correct. Let's try this: color the second one <scene name='User:Nir_London/FunHunt/1stp_2_blue/1' target='2'>blue</scene>.

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==References==

1.
2.

User:Nir London/FunHunt

2008-09-14T17:26:22Z

Nir London:

<applet load='1STF_2.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
<applet load='1STF_1.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are two docking models for the complex of recombinant human Stefin B with cysteine proteinase Papain. One of the models is correct while the other is incorrect, can you tell which is which ? <scene name='User:Nir_London/FunHunt/1stf_correct/1'>Click here</scene> to color the correct model blue and find out if you were correct.

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==Why do we need it ?==
Protein complexes is very important

==References==

1.
2.

User:Nir London/FunHunt

2008-09-14T17:16:44Z

Nir London:

<applet load='1STF_2.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
<applet load='1STF_1.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are two docking models for the complex of recombinant human Stefin B with cysteine proteinase Papain. One of the models is correct while the other is incorrect, can you tell which is which ?

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==Why do we need it ?==
Protein complexes is very important

==References==

1.
2.

User:Nir London/FunHunt

2008-09-14T15:40:04Z

Nir London:

<applet load='1STF_2.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
<applet load='1STF_1.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are presented two docking models for the complex of ... One of the models is correct while the other is in-correct, can you tell which is which ?

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==Why do we need it ?==
Protein complexes is very important

==References==

1.
2.

File:1STF 2.pdb

2008-09-14T15:39:01Z

Nir London:

File:1STF 1.pdb

2008-09-14T15:38:24Z

Nir London:

User:Nir London/FunHunt

2008-09-14T15:36:22Z

Nir London:

<applet load='1STF_false.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
<applet load='1STF_true.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are presented two docking models for the complex of ... One of the models is correct while the other is in-correct, can you tell which is which ?

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==Why do we need it ?==
Protein complexes is very important

==References==

1.
2.

User:Nir London/FunHunt

2008-09-14T15:34:36Z

Nir London: /* FunHunt */

<applet load='1stf_false.pdb' size='300' frame='true' align='right' caption='this is not how 1stf looks like' />

<applet load='1STF_false.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
<applet load='1STF_true.pdb' size='300' frame='true' align='left' caption='Insert caption here' />

==Quiz==
To the right and left are presented two docking models for the complex of ... One of the models is correct while the other is in-correct, can you tell which is which ?

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==Why do we need it ?==
why not ?

File:1STF true.pdb

2008-09-14T15:31:11Z

Nir London: This is a CORRECT docking model of the complex from 1stf

This is a CORRECT docking model of the complex from 1stf

File:1STF false.pdb

2008-09-14T15:30:43Z

Nir London: This is a WRONG docking model of the complex from 1stf

This is a WRONG docking model of the complex from 1stf

File:1STF.pdb

2008-09-14T15:11:24Z

Nir London: a WRONG model of the complex in 1STF pdb, part of the FunHunt training set

a WRONG model of the complex in 1STF pdb, part of the FunHunt training set

User:Nir London/FunHunt

2008-09-14T15:10:18Z

Nir London: /* FunHunt */

<applet load='1stf_false.pdb' size='300' frame='true' align='right' caption='this is not how 1stf looks like' />

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

==Why do we need it ?==
why not ?

User:Nir London/FunHunt

2008-09-14T14:59:31Z

Nir London: New page: ==FunHunt== FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on th...

==FunHunt==
FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).

{{STRUCTURE_1ak4 | PDB=1ak4 | SCENE= }}

==Why do we need it ?==
why not ?