ROSETTA使用技巧随笔--RosettaLigand Docking

时间不充分，简单记录下自己实践过程中的做法:

1. 首先，非标准残基都需要转换成.params文件，使用 <path-to-Rosetta>/main/source/scripts/python/public/molfile_to_params.py -n TPP TPP.mol2 --chain=F --clobber --keep_names 转换，此命令会产生TPP_0001.pdb和TPP.params两个文件；

2. 其次，如果配体需要进行构象搜索，可以使用obabel，这个免费且简单，见博客http://www.cnblogs.com/wq242424/p/8231600.html，需要做限制性构象搜索的话，就比较难了，我用的是schrodinger的conformational search里的高级搜索；

3. 如果经过上一步产生了ligand_conformers.sdf，就需要为 <path-to-Rosetta>/main/source/scripts/python/public/molfile_to_params.py -n GAD -p GAD --chain=X --center=-31,-35.5,8 --clobber --keep_names --conformers-in-one-file GAD_confs.sdf 命令多加一个参数 --conformers-in-one-file GAD_confs.sdf ，这个参数会在产生的.params文件末尾加一句 PDB_ROTAMERS GAD_conformers.pdb 来表明你的多重构象的文件，此命令会产生GAD.pdb，GAD.params和GAD_conformers.pdb三个文件，其中GAD.pdb是以conformers中第一个构象为结构；

4. 多底物对接的问题，经过查阅手册和论坛，得出的结论是通过控制需要dock的链("X/Y/F/。。。")来指定需要对接的小分子，比如我要对接TPP和GAD，就需要在single movers后面及前面LIGAND_AREAS和INTERFACE_BUILDERS那里指定分别对“F”和“X”链进行dock，并在MOVERS处指定两底物分子分别对应的操作，options不必特意根据双底物改变，下面给出了我做的两个XML文件的示例；

5. StartFrom,Transform,Translate和Rotate的差别和比较。StartFrom是在底物不在蛋白口袋内部，需要程序先将底物以Coordinates为基准放到口袋中的程序；Transform是使用蒙特卡洛的方法，对对接过程的底物和蛋白小分子随机取样的过程；Translate和Rotate则是对处于口袋中的小分子进行平移旋转的操作。底物在蛋白口袋中时，就可以不使用StartFrom；使用Transform时，则需要指定GRID。

6. 至于下面的high_resolution_dock XML文件，用途是在你已经知道你的底物的位置的情况下，对底物及周边残基进行高分辨率的对接，与其说对接，可能说packing和minimizing更恰当，因为它是对周围的残基优化的同时变换底物的构象，以求找到最优结果。

分享一下自己的两个xml文件及对应的flags：

low_resolution_dock+high_resolution_dock

This protocol will simply do low-resolution followed by high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ligand_soft_rep weights="ligand_soft_rep">
		</ligand_soft_rep>
		<hard_rep weights="ligand">
		</hard_rep>
	</SCOREFXNS>
	<LIGAND_AREAS>
		<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
		<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
		<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
	</LIGAND_AREAS>
	<INTERFACE_BUILDERS>
		<side_chain_for_docking ligand_areas="docking_sidechain_X"/>
		<side_chain_for_final ligand_areas="final_sidechain_X"/>
		<backbone ligand_areas="final_backbone_X" extension_window="3"/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
		<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
	</MOVEMAP_BUILDERS>
	<MOVERS>
	single movers		
		<StartFrom name="start_from_X" chain="X">
			<Coordinates x="-31" y="-35.5" z="8"/>        
		</StartFrom>
		<CompoundTranslate name="compound_translate" randomize_order="false" allow_overlap="false">
			<Translate chain="X" distribution="uniform" angstroms="2.0" cycles="50"/>
		</CompoundTranslate>
		<Rotate name="rotate_X" chain="X" distribution="uniform" degrees="360" cycles="500"/>
		<SlideTogether name="slide_together" chains="X"/>
		<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
		<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
		<InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep"/>
	compound movers
		<ParsedProtocol name="low_res_dock">
			<Add mover_name="start_from_X"/>
			<Add mover_name="compound_translate"/>
			<Add mover_name="rotate_X"/>
			<Add mover_name="slide_together"/>
		</ParsedProtocol>
		<ParsedProtocol name="high_res_dock">
			<Add mover_name="high_res_docker"/>
			<Add mover_name="final"/>
		</ParsedProtocol>
	</MOVERS>
	<PROTOCOLS>
		<Add mover_name="low_res_dock"/>
		<Add mover_name="high_res_dock"/>
		<Add mover_name="add_scores"/>
	</PROTOCOLS>
</ROSETTASCRIPTS>

对应的flag options文件：

-in:file:s inputs_GAD/GALS_TPP_GAD.pdb
-in:file:extra_res_fa inputs_GAD/TPP.params inputs_GAD/GAD.params

-packing
	-ex1
	-ex2aro
	-ex2 
	-no_optH false
	-flip_HNQ true
	-ignore_ligand_chi true
	
-parser
	-protocol inputs_GAD/ligand_dock.xml

-out
	-path:all outputs_GAD
	-nstruct 1000
	-overwrite

high_resolution_dock_only

This protocol will simply do high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ligand_soft_rep weights="ligand_soft_rep">
		</ligand_soft_rep>
		<hard_rep weights="ligand">
		</hard_rep>
	</SCOREFXNS>
	<LIGAND_AREAS>
		<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
		<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
		<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
	</LIGAND_AREAS>
	<INTERFACE_BUILDERS>
		<side_chain_for_docking ligand_areas="docking_sidechain_X"/>
		<side_chain_for_final ligand_areas="final_sidechain_X"/>
		<backbone ligand_areas="final_backbone_X" extension_window="3"/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
		<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
	</MOVEMAP_BUILDERS>
	<SCORINGGRIDS ligand_chain="X" width="15">
		<classic grid_type="ClassicGrid" weight="1.0"/>
	</SCORINGGRIDS>
	<MOVERS>
		<Transform name="transform" chain="X"box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/>
		<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
		<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
		<InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep"/>
	</MOVERS>
	<PROTOCOLS>
		<Add mover_name="transform"/>
		<Add mover_name="high_res_docker"/>
		<Add mover_name="final"/>
		<Add mover_name="add_scores"/>
	</PROTOCOLS>
</ROSETTASCRIPTS>

对应的flag_options文件：

-in:file:s inputs_IMA/GALS_IMA.pdb
-in:file:extra_res_fa inputs_IMA/IMA.params

-packing
	-ex1
	-ex2aro
	-ex2 
	-no_optH false
	-flip_HNQ true
	-ignore_ligand_chi true
	
-parser
	-protocol inputs_IMA/ligand_dock.xml

-out
	-path:all outputs_IMA
	-nstruct 1000
	-overwrite

多底物对接（两个小分子的链分别对应“X”和“F”）

 1. 手动指定两个小分子（“X”，“F”）的位置（使用StartFrom mover指定，对应的Coordinates）

This protocol will simply do low-resolution followed by high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ligand_soft_rep weights="ligand_soft_rep">
		</ligand_soft_rep>
		<hard_rep weights="ligand">
		</hard_rep>
	</SCOREFXNS>
	<LIGAND_AREAS>
		<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
		<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
		<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
		
		<docking_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
		<final_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
		<final_backbone_F chain="F" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
	</LIGAND_AREAS>
	<INTERFACE_BUILDERS>
		<side_chain_for_docking ligand_areas="docking_sidechain_X,docking_sidechain_F"/>
		<side_chain_for_final ligand_areas="final_sidechain_X,final_sidechain_F"/>
		<backbone ligand_areas="final_backbone_X,final_backbone_F" extension_window="3"/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
		<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
	</MOVEMAP_BUILDERS>
	<MOVERS>
	single movers_X		
		<StartFrom name="start_from_X" chain="X">
			<Coordinates x="-31" y="-35.5" z="8"/>        
		</StartFrom>
		<StartFrom name="start_from_F" chain="F">
			<Coordinates x="-27.26" y="-34.56" z="4.87"/>        
		</StartFrom>
		<CompoundTranslate name="compound_translate" randomize_order="false" allow_overlap="false">
			<Translate chain="X" distribution="uniform" angstroms="2.0" cycles="50"/>
			<Translate chain="F" distribution="uniform" angstroms="2.0" cycles="50"/>
		</CompoundTranslate>
		<Rotate name="rotate_X" chain="X" distribution="uniform" degrees="360" cycles="500"/>
		<Rotate name="rotate_F" chain="F" distribution="uniform" degrees="360" cycles="500"/>
		
		<SlideTogether name="slide_together" chains="X,F"/>
		<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
		<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
		<InterfaceScoreCalculator name="add_scores" chains="X,F" scorefxn="hard_rep"/>
		
	compound movers
		<ParsedProtocol name="low_res_dock">
			<Add mover_name="start_from_X"/>
			<Add mover_name="start_from_F"/>
			<Add mover_name="compound_translate"/>
			<Add mover_name="rotate_X"/>
			<Add mover_name="rotate_F"/>			
			<Add mover_name="slide_together"/>
		</ParsedProtocol>
		<ParsedProtocol name="high_res_dock">
			<Add mover_name="high_res_docker"/>
			<Add mover_name="final"/>
		</ParsedProtocol>
	</MOVERS>
	<PROTOCOLS>
		<Add mover_name="low_res_dock"/>
		<Add mover_name="high_res_dock"/>
		<Add mover_name="add_scores"/>		
	</PROTOCOLS>
</ROSETTASCRIPTS> 

 2. 其中一个小分子（“F”）位置已知，另一个小分子（“X”）的位置需要指定（首先需使用SCORINGGRIDS为已知位置的小分子指定盒子，然后使用Transform指定其动作模式）

This protocol will simply do low-resolution followed by high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ligand_soft_rep weights="ligand_soft_rep">
		</ligand_soft_rep>
		<hard_rep weights="ligand">
		</hard_rep>
	</SCOREFXNS>
	<LIGAND_AREAS>
		<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
		<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
		<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
		
		<docking_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
		<final_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
		<final_backbone_F chain="F" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
	</LIGAND_AREAS>
	<INTERFACE_BUILDERS>
		<side_chain_for_docking ligand_areas="docking_sidechain_X,docking_sidechain_F"/>
		<side_chain_for_final ligand_areas="final_sidechain_X,final_sidechain_F"/>
		<backbone ligand_areas="final_backbone_X,final_backbone_F" extension_window="3"/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
		<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
	</MOVEMAP_BUILDERS>
	<SCORINGGRIDS ligand_chain="F" width="15">
		<classic grid_type="ClassicGrid" weight="1.0"/>
	</SCORINGGRIDS>
	<MOVERS>
	single movers_X		
		<StartFrom name="start_from_X" chain="X">
			<Coordinates x="-31" y="-35.5" z="8"/>        
		</StartFrom>
		<Transform name="transform_F" chain="F" box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/>
		<CompoundTranslate name="compound_translate" randomize_order="false" allow_overlap="false">
			<Translate chain="X" distribution="uniform" angstroms="2.0" cycles="50"/>
			<Translate chain="F" distribution="uniform" angstroms="2.0" cycles="50"/>
		</CompoundTranslate>
		<Rotate name="rotate_X" chain="X" distribution="uniform" degrees="360" cycles="500"/>
		<Rotate name="rotate_F" chain="F" distribution="uniform" degrees="360" cycles="500"/>
		
		<SlideTogether name="slide_together" chains="X,F"/>
		<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
		<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
		<InterfaceScoreCalculator name="add_scores" chains="X,F" scorefxn="hard_rep"/>
		
	compound movers
		<ParsedProtocol name="low_res_dock">
			<Add mover_name="start_from_X"/>
			<Add mover_name="transform_F"/>
			<Add mover_name="compound_translate"/>
			<Add mover_name="rotate_X"/>
			<Add mover_name="rotate_F"/>			
			<Add mover_name="slide_together"/>
		</ParsedProtocol>
		<ParsedProtocol name="high_res_dock">
			<Add mover_name="high_res_docker"/>
			<Add mover_name="final"/>
		</ParsedProtocol>
	</MOVERS>
	<PROTOCOLS>
		<Add mover_name="low_res_dock"/>
		<Add mover_name="high_res_dock"/>
		<Add mover_name="add_scores"/>		
	</PROTOCOLS>
</ROSETTASCRIPTS>