FlexPepDock - Revision history

Frodo at 03:39, 14 February 2014

2014-02-14T03:39:09Z

← Older revision		Revision as of 03:39, 14 February 2014
Line 136:		Line 136:
	=Acknowlegements=		=Acknowlegements=
	Many thanks to Nir for compiling Rosetta on our server, the introduction into FlexPepDock and the fp* scripts.		Many thanks to Nir for compiling Rosetta on our server, the introduction into FlexPepDock and the fp* scripts.


			[[Category:Tutorials]]
			[[Category:Docking]]

Oliv Eidam: /* 1. Create peptide coordinates in Pymol */

2013-05-17T17:54:26Z

1. Create peptide coordinates in Pymol

← Older revision		Revision as of 17:54, 17 May 2013
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	Save molecule.		Save molecule.
	Do NOT add a amine at the N-terminus and do NOT add a C-terminal carboxylate to the pymol coordinates!		Do NOT add a amine at the N-terminus and do NOT add a C-terminal carboxylate to the pymol coordinates!
	'''Important note:''' FlexPepDock does not change your ~~Psi~~ angles, so make sure that a proline is in trans if that's what you want!!		'''Important note:''' FlexPepDock does not change your Omega angles, so make sure that a proline is in trans if that's what you want!!


	==2. Dock peptide coordinates in Pymol to generate a starting model for FlexPepDock ==		==2. Dock peptide coordinates in Pymol to generate a starting model for FlexPepDock ==

Oliv Eidam: /* Acknowlegements */

2013-05-08T00:09:17Z

Acknowlegements

← Older revision		Revision as of 00:09, 8 May 2013
Line 136:		Line 136:

	=Acknowlegements=		=Acknowlegements=
	Many thanks to Nir for the introduction into FlexPepDock.		Many thanks to Nir for compiling Rosetta on our server, the introduction into FlexPepDock and the fp* scripts.

Oliv Eidam at 23:46, 7 May 2013

2013-05-07T23:46:35Z

← Older revision		Revision as of 23:46, 7 May 2013
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	./rescore_batch.csh		./rescore_batch.csh

	~~The~~ orange output model had a backbone RMSD of 1.9 Angstroem (3.4 A over HA all atoms), which is a freaking good prediction. A few models had RMSD values as low as 1.2 A, but scored worse.		In my prospective prediction, the orange output model had a backbone RMSD of 1.9 Angstroem (3.4 A over HA all atoms), which is a freaking good prediction. The the backbones align perfectly over the last four amino acids, and the two arginines at the N-terminus are actually (and surprisingly) not perfectly ordered in the crystal structure. <br>
			As a side note: a few models had RMSD values as low as 1.2 A, but scored worse.

Oliv Eidam at 23:41, 7 May 2013

2013-05-07T23:41:51Z

← Older revision		Revision as of 23:41, 7 May 2013
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	=FlexPepDock: Wanna dock a peptide? Use FlexPepDock!=		=FlexPepDock: Wanna dock a peptide? Use FlexPepDock!=

			[[File:Rec w arg327.png\|thumb\|right\|alt=X-ray structure of Neurotensin receptor. The C-terminus of NT(8-13) was predicted to interact with Arg327, which is depicted with spheres. \|X-ray structure of Neurotensin receptor. The C-terminus of NT(8-13) was predicted to interact with Arg327, which is depicted with spheres.]]

	Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest way to do that is to use the online server: <br>		Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest way to do that is to use the online server: <br>
	http://flexpepdock.furmanlab.cs.huji.ac.il		http://flexpepdock.furmanlab.cs.huji.ac.il


	If you want to run FlexPepDock locally, follow the steps below. <br>		If you want to run FlexPepDock locally, follow the steps below. <br>
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	==1. Create peptide coordinates in Pymol==		==1. Create peptide coordinates in Pymol==

			[[File:Rec w input peptides.png\|thumb\|right\|alt=Backbone representation of manually docked starting peptides (orange and green). \|Backbone representation of manually docked starting peptides (orange and green).]]

	You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>		You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>
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	==4. Run FlexPepDock on Cluster using submit_fpdock.sh==		==4. Run FlexPepDock on Cluster using submit_fpdock.sh==

			[[File:Rec w output peptides.png\|thumb\|right\|alt=Backbone representation of best scoring output peptides (orange and green). \|Backbone representation of best scoring output peptides (orange and green).]]

	Run FlexPepDock on Cluster using submit_fpdock.sh (see code below):		Run FlexPepDock on Cluster using submit_fpdock.sh (see code below):
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	==5. Analyze output models==		==5. Analyze output models==

			[[File:Pose1 input output vs xray.png\|thumb\|right\|alt=Comparison of native peptide conformation (slate) to best scoring output model (orange). The backbone of the starting peptide is depicted in yellow. \|Comparison of native peptide conformation (slate) to best scoring output model (orange). The backbone of the starting peptide is depicted in yellow.]]

	FlexPepDock outputs a pdb, a score file (.sc) and a log file (log) for each model requested. The score files is a tab-delimited file with many scores and other interesting numbers like Interface buried surface area (I_bsa), number of hydrogen bonds (I_hb), score for the Interface (I_sc) and a score for the peptide (pep_sc). Your main interest is most likely the total score (total_score).		FlexPepDock outputs a pdb, a score file (.sc) and a log file (log) for each model requested. The score files is a tab-delimited file with many scores and other interesting numbers like Interface buried surface area (I_bsa), number of hydrogen bonds (I_hb), score for the Interface (I_sc) and a score for the peptide (pep_sc). Your main interest is most likely the total score (total_score).
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	echo $file":" `awk 'NR==3 {print $2}' $file`		echo $file":" `awk 'NR==3 {print $2}' $file`
	end		end

			In my prospective peptide docking, the best scoring output model starting from the orange pose had a total score of -324, which was better than the score of the green starting pose (-316).


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	Then run rescore_batch.csh (see code below):		Then run rescore_batch.csh (see code below):
	./rescore_batch.csh		./rescore_batch.csh

			The orange output model had a backbone RMSD of 1.9 Angstroem (3.4 A over HA all atoms), which is a freaking good prediction. A few models had RMSD values as low as 1.2 A, but scored worse.


	'''Code of rescore_batch.csh:'''		'''Code of rescore_batch.csh:'''

Oliv Eidam at 23:12, 7 May 2013

2013-05-07T23:12:58Z

← Older revision		Revision as of 23:12, 7 May 2013
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	In my example I docked the hexapeptide NT(8-13) with the sequence RRPYIL into the neurotensin receptor. I did this prospectively, without having looked at the bound peptide conformation before doing this. All I knew was that the C-terminal carboxylate interacts with Arg327 ([http://www.jbc.org/content/275/1/328 Barroso et al, JBC, 2000]) and that the peptide adopts an extended conformation ([http://www.pnas.org/content/100/19/10706 Luca et al, PNAS, 2003]).		In my example I docked the hexapeptide NT(8-13) with the sequence RRPYIL into the neurotensin receptor. I did this prospectively, without having looked at the bound peptide conformation before doing this. All I knew was that the C-terminal carboxylate interacts with Arg327 ([http://www.jbc.org/content/275/1/328 Barroso et al, JBC, 2000]) and that the peptide adopts an extended conformation ([http://www.pnas.org/content/100/19/10706 Luca et al, PNAS, 2003]).

	==1. Create peptide coordinates==		==1. Create peptide coordinates in Pymol==

	You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>		You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>
Line 16:		Line 16:


	==2. Dock peptide coordinates ~~manually~~ to generate a starting model for FlexPepDock ==		==2. Dock peptide coordinates in Pymol to generate a starting model for FlexPepDock ==

	You need a rough starting peptide model for FlexPepDock. The peptide starting model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above in Pymol into to the receptor by switching to Editing Mode, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.		You need a rough starting peptide model for FlexPepDock. The peptide starting model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above in Pymol into to the receptor by switching to Editing Mode, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.

	Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.		Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.


	==3. Run prepack.sh==		==3. Run prepack.sh==
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	echo $file":" `awk 'NR==3 {print $2}' $file`		echo $file":" `awk 'NR==3 {print $2}' $file`
	end		end


	==6. Calculate RMSD values compared to native structure==		==6. Calculate RMSD values compared to native structure==

Oliv Eidam at 23:11, 7 May 2013

2013-05-07T23:11:34Z

← Older revision		Revision as of 23:11, 7 May 2013
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	==2. ~~Create input model~~ peptide coordinates==		==2. Dock peptide coordinates manually to generate a starting model for FlexPepDock ==

	You need a rough ~~input~~ peptide model for FlexPepDock. The peptide ~~input~~ model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above into to the receptor by switching to Editing Mode ~~in Pymol~~, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.		You need a rough starting peptide model for FlexPepDock. The peptide starting model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above in Pymol into to the receptor by switching to Editing Mode, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.

	Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.		Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.

Oliv Eidam at 23:08, 7 May 2013

2013-05-07T23:08:23Z

← Older revision		Revision as of 23:08, 7 May 2013
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	# ls -1 *.pdb > list_of_pdbs.txt		# ls -1 *.pdb > list_of_pdbs.txt

	This script takes a few minutes to run and outputs a file called log.rescore_list. ~~Print~~ the scores, backbone RMSDs and model name, sorted by backbone RMSD:		This script takes a few minutes to run and outputs a file called log.rescore_list. For each model, you can print the scores, backbone RMSDs and model name, sorted by backbone RMSD, by typing this command:

	awk '{print $2, $41, $53}' rescore_list.score.sc \| sort -rgk 2		awk '{print $2, $41, $53}' rescore_list.score.sc \| sort -rgk 2


			=Acknowlegements=
			Many thanks to Nir for the introduction into FlexPepDock.

Oliv Eidam: Undo revision 5500 by Oliv Eidam (talk)

2013-05-07T23:06:07Z

Undo revision 5500 by Oliv Eidam (talk)

← Older revision		Revision as of 23:06, 7 May 2013
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	==FlexPepDock: Wanna dock a peptide? Use FlexPepDock!==		=FlexPepDock: Wanna dock a peptide? Use FlexPepDock!=

	Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest way to do that is to use the online server: <br>		Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest way to do that is to use the online server: <br>
Line 8:		Line 8:
	In my example I docked the hexapeptide NT(8-13) with the sequence RRPYIL into the neurotensin receptor. I did this prospectively, without having looked at the bound peptide conformation before doing this. All I knew was that the C-terminal carboxylate interacts with Arg327 ([http://www.jbc.org/content/275/1/328 Barroso et al, JBC, 2000]) and that the peptide adopts an extended conformation ([http://www.pnas.org/content/100/19/10706 Luca et al, PNAS, 2003]).		In my example I docked the hexapeptide NT(8-13) with the sequence RRPYIL into the neurotensin receptor. I did this prospectively, without having looked at the bound peptide conformation before doing this. All I knew was that the C-terminal carboxylate interacts with Arg327 ([http://www.jbc.org/content/275/1/328 Barroso et al, JBC, 2000]) and that the peptide adopts an extended conformation ([http://www.pnas.org/content/100/19/10706 Luca et al, PNAS, 2003]).

	===1. Create peptide coordinates===		==1. Create peptide coordinates==

	You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>		You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>
Line 16:		Line 16:


	===2. Create input model peptide coordinates===		==2. Create input model peptide coordinates==

	You need a rough input peptide model for FlexPepDock. The peptide input model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above into to the receptor by switching to Editing Mode in Pymol, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.		You need a rough input peptide model for FlexPepDock. The peptide input model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above into to the receptor by switching to Editing Mode in Pymol, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.
Line 22:		Line 22:
	Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.		Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.

	===3. Run prepack.sh===		==3. Run prepack.sh==

	Run prepack.sh (see code below):		Run prepack.sh (see code below):
Line 44:		Line 44:


	===4. Run FlexPepDock on Cluster using submit_fpdock.sh===		==4. Run FlexPepDock on Cluster using submit_fpdock.sh==

	Run FlexPepDock on Cluster using submit_fpdock.sh (see code below):		Run FlexPepDock on Cluster using submit_fpdock.sh (see code below):
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	===5. Analyze output models===		==5. Analyze output models==

	FlexPepDock outputs a pdb, a score file (.sc) and a log file (log) for each model requested. The score files is a tab-delimited file with many scores and other interesting numbers like Interface buried surface area (I_bsa), number of hydrogen bonds (I_hb), score for the Interface (I_sc) and a score for the peptide (pep_sc). Your main interest is most likely the total score (total_score).		FlexPepDock outputs a pdb, a score file (.sc) and a log file (log) for each model requested. The score files is a tab-delimited file with many scores and other interesting numbers like Interface buried surface area (I_bsa), number of hydrogen bonds (I_hb), score for the Interface (I_sc) and a score for the peptide (pep_sc). Your main interest is most likely the total score (total_score).
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	end		end

	===6. Calculate RMSD values compared to native structure===		==6. Calculate RMSD values compared to native structure==

			FlexPepDock automatically outputs RMSD values of the models compared to the input structure (rmsALL, rmsBB etc.). But if you know the native structure, you are probably interested how the models compare to the native structure.

			You can calculate RMSD values for each model compared to the native structure using the script rescore_batch.csh.
			First, you have to generate a list of pdb IDs for which you want to generate RMSDs compared to the native structure:

			ls -1 *.pdb > list_of_pdbs.txt

			Then run rescore_batch.csh (see code below):
			./rescore_batch.csh

			'''Code of rescore_batch.csh:'''

			#!/bin/csh

			#-s starting
			#-native: reference for rmsd calc
			# -l list file

			~londonir/rosetta/rosetta_source/bin/FlexPepDocking.static.linuxgccrelease -l list_of_pdbs.txt -database /raid1/people/londonir/rosetta/rosetta_database -native 4GRV_AB_ATOM.pdb -out:prefix rescore_list'.' -flexpep_score_only -out:pdb false > log.rescore_list


			#create list with pdbs
			# ls -1 *.pdb > list_of_pdbs.txt

			This script takes a few minutes to run and outputs a file called log.rescore_list. Print the scores, backbone RMSDs and model name, sorted by backbone RMSD:

			awk '{print $2, $41, $53}' rescore_list.score.sc \| sort -rgk 2

Oliv Eidam at 22:02, 7 May 2013

2013-05-07T22:02:25Z

← Older revision		Revision as of 22:02, 7 May 2013
Line 1:		Line 1:
	=FlexPepDock: Wanna dock a peptide? Use FlexPepDock!=		==FlexPepDock: Wanna dock a peptide? Use FlexPepDock!==

	Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest way to do that is to use the online server: <br>		Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest way to do that is to use the online server: <br>
Line 8:		Line 8:
	In my example I docked the hexapeptide NT(8-13) with the sequence RRPYIL into the neurotensin receptor. I did this prospectively, without having looked at the bound peptide conformation before doing this. All I knew was that the C-terminal carboxylate interacts with Arg327 ([http://www.jbc.org/content/275/1/328 Barroso et al, JBC, 2000]) and that the peptide adopts an extended conformation ([http://www.pnas.org/content/100/19/10706 Luca et al, PNAS, 2003]).		In my example I docked the hexapeptide NT(8-13) with the sequence RRPYIL into the neurotensin receptor. I did this prospectively, without having looked at the bound peptide conformation before doing this. All I knew was that the C-terminal carboxylate interacts with Arg327 ([http://www.jbc.org/content/275/1/328 Barroso et al, JBC, 2000]) and that the peptide adopts an extended conformation ([http://www.pnas.org/content/100/19/10706 Luca et al, PNAS, 2003]).

	==1. Create peptide coordinates==		===1. Create peptide coordinates===

	You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>		You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis->Mutate to Arg->Apply). <br>
Line 16:		Line 16:


	==2. Create input model peptide coordinates==		===2. Create input model peptide coordinates===

	You need a rough input peptide model for FlexPepDock. The peptide input model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above into to the receptor by switching to Editing Mode in Pymol, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.		You need a rough input peptide model for FlexPepDock. The peptide input model should be within 5 Angstroem RMSD to the native structure. You can manually dock your peptide created above into to the receptor by switching to Editing Mode in Pymol, and dragging/rotating the peptide by holding the Shift-Button and Middle and Left-Mouse button, respectively. Don't worry about clashes of the peptide with the protein: the most important thing is that the backbone is within 5 Anstroem of the native structure.
Line 22:		Line 22:
	Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.		Save the docked peptide coordinates and '''add them at the below of the PDB coordinates''' of the apo receptor structure. It is important to add them below the receptor coordinates, separated by a TER statement. Also, there should be no END statements.

	==3. Run prepack.sh==		===3. Run prepack.sh===

	Run prepack.sh (see code below):		Run prepack.sh (see code below):
Line 44:		Line 44:


	==4. Run FlexPepDock on Cluster using submit_fpdock.sh==		===4. Run FlexPepDock on Cluster using submit_fpdock.sh===

	Run FlexPepDock on Cluster using submit_fpdock.sh (see code below):		Run FlexPepDock on Cluster using submit_fpdock.sh (see code below):
Line 76:		Line 76:


	==5. Analyze output models==		===5. Analyze output models===

	FlexPepDock outputs a pdb, a score file (.sc) and a log file (log) for each model requested. The score files is a tab-delimited file with many scores and other interesting numbers like Interface buried surface area (I_bsa), number of hydrogen bonds (I_hb), score for the Interface (I_sc) and a score for the peptide (pep_sc). Your main interest is most likely the total score (total_score).		FlexPepDock outputs a pdb, a score file (.sc) and a log file (log) for each model requested. The score files is a tab-delimited file with many scores and other interesting numbers like Interface buried surface area (I_bsa), number of hydrogen bonds (I_hb), score for the Interface (I_sc) and a score for the peptide (pep_sc). Your main interest is most likely the total score (total_score).
Line 89:		Line 89:
	end		end

	==6. Calculate RMSD values compared to native structure==		===6. Calculate RMSD values compared to native structure===