LigandBindingAssemblyMover

LigandBindingAssemblyMover is a derived AppendAssemblyMover that is intended to build new contacts to a partially coordinated ligand while simultaneously building new protein backbone using SEWING.

Description

LigandBindingAssemblyMover takes a partial ligand binding site and its ligand and, given user-provided information on how the ligand should be coordinated, adds new structural elements that will be able to complete the ligand's coordination with the correct geometry. It also makes any necessary mutations for this coordination and outputs PDBInfoRemarks indicating all coordinating residues.

Usage

NOTE: This is currently unavailable but will be automatically updated when the new version of SEWING is merged.

Autogenerated Tag Syntax Documentation:

AssemblyMover designed to add contacts to specified ligand atoms and then build an assembly around the ligand.

<LigandBindingAssemblyMover name="(&string;)" start_temperature="(0.6 &real;)"
        end_temperature="(0.6 &real;)" add_probability="(0.05 &real;)"
        delete_probability="(0.005 &real;)"
        conformer_switch_probability="(0 &real;)"
        window_width="(4 &positive_integer;)"
        minimum_cycles="(10000 &non_negative_integer;)"
        maximum_cycles="(100000 &non_negative_integer;)"
        model_file_name="(&string;)" hashed="(false &bool;)"
        edge_file_name="(&string;)" max_segments="(100 &non_negative_integer;)"
        max_segment_length="(100 &non_negative_integer;)"
        output_pose_per_move="(false &bool;)"
        recover_lowest_assembly="(true &bool;)"
        recursive_depth="(1 &non_negative_integer;)"
        pose_segment_starts="(&int_cslist;)" pose_segment_ends="(&int_cslist;)"
        pose_segment_dssp="(&string;)" strict_dssp_changes="(false &bool;)"
        set_segments_from_dssp="(false &bool;)" match_segments="(&int_cslist;)"
        partner_pdb="(&string;)"
        required_resnums="(&refpose_enabled_residue_number_cslist;)"
        max_recursion="(1 &non_negative_integer;)"
        modifiable_terminus="(B &string;)" output_partner="(true &bool;)"
        extend_mode="(false &bool;)" start_node_vital_segments="(all &string;)"
        required_selector="(&string;)" distance_cutoff="(10.0 &real;)"
        segment_distance_cutoff="(1 &non_negative_integer;)"
        binding_cycles="(1000 &non_negative_integer;)"
        build_site_only="(false &bool;)" >
    <AssemblyScorers >
        <InterModelMotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <IntraDesignTerminusMotifScorer name="(&string;)" weight="(1.0 &real;)"
                optimum_distance="(&real;)" maximum_unpenalized_variance="(&real;)" />
        <LigandScorer name="(&string;)" weight="(1.0 &real;)"
                ligand_interaction_cutoff_distance="(5.0 &real;)" />
        <MotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <PartnerMotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <SegmentContactOrderScorer name="(&string;)" weight="(1.0 &real;)" />
        <StartingNodeMotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <SubsetPartnerMotifScorer name="(&string;)" weight="(1.0 &real;)"
                region_start="(1 &non_negative_integer;)"
                region_end="(2 &non_negative_integer;)" />
        <TerminusMotifScorer name="(&string;)" weight="(1.0 &real;)"
                partner_residue="(&non_negative_integer;)" optimum_distance="(&real;)"
                maximum_unpenalized_variance="(&real;)" terminus="(&string;)" />
        <TopNMotifScorer name="(&string;)" weight="(1.0 &real;)"
                scores_to_keep="(1 &non_negative_integer;)" />
    </AssemblyScorers>
    <AssemblyRequirements >
        <ClashRequirement name="(&string;)"
                maximum_clashes_allowed="(0 &non_negative_integer;)"
                clash_radius="(4.0 &real;)" />
        <DsspSpecificLengthRequirement name="(&string;)" dssp_code="(X &dssp_enum;)"
                maximum_length="(100 &non_negative_integer;)"
                minimum_length="(0 &non_negative_integer;)" />
        <KeepLigandContactsRequirement name="(&string;)"
                contact_distance_cutoff="(2.5 &real;)" />
        <LengthInResiduesRequirement name="(&string;)"
                maximum_length="(10000 &non_negative_integer;)"
                minimum_length="(0 &non_negative_integer;)" />
        <LigandClashRequirement name="(&string;)"
                maximum_clashes_allowed="(0 &non_negative_integer;)"
                clash_radius="(4.0 &real;)" />
        <NonTerminalStartingSegmentRequirement />
        <SizeInSegmentsRequirement name="(&string;)"
                maximum_size="(10000 &non_negative_integer;)"
                minimum_size="(0 &non_negative_integer;)" />
    </AssemblyRequirements>
    <Ligands >
        <Ligand partner_ligand="(false &bool;)" pdb_conformers="(&string;)"
                alignment_atoms="(&string;)" auto_detect_contacts="(true &bool;)"
                ligand_resnum="(&refpose_enabled_residue_number;)"
                ligand_selector="(&string;)" >
            <Contact partner_contact="(false &bool;)"
                    contact_resnum="(&refpose_enabled_residue_number;)"
                    ligand_atom_name="(&string;)" contact_atom_name="(&string;)" />
            <Coordination coordination_files="(&string;)"
                    geometry_score_threshold="(1 &real;)" >
                <IdealContacts distance="(&real;)" angle="(109.5 &real;)"
                        dihedral_1="(30 &real;)" dihedral_2="(30 &real;)"
                        max_coordinating_atoms="(&non_negative_integer;)"
                        ligand_atom_name="(&string;)" />
            </Coordination>
        </Ligand>
    </Ligands>
</LigandBindingAssemblyMover>

start_temperature: Temperature at start of simulated annealing
end_temperature: Temperature at end of simulated annealing
add_probability: Probability of adding a triplet of segments at any given step during assembly
delete_probability: Probability of deleting a terminal triplet of segments at any given step during assembly
conformer_switch_probability: Probability of switching ligand conformers during assembly. This should only be used if a ligand is present AND if you have provided conformers for that ligand.
window_width: Required number of overlapping residues for two segments to be considered a match. Used in hashless SEWING only (for hashed SEWING, this is determined by the hasher settings used when generating the edge file).
minimum_cycles: Minimum number of Monte Carlo cycles for assembly before completion requirements are checked.
maximum_cycles: Maximum number of Monte Carlo cycles for assembly before forced termination.
model_file_name: (REQUIRED) Path to file defining segments to use during assembly
hashed: Use the hasher during assembly to check overlap of all atoms? Requires an input edge file.
edge_file_name: Path to edge file to use during assembly (only used if hashed is set to true)
max_segments: Maximum number of segments to include in the final assembly
max_segment_length: Maximum number of residues to include in a segment
output_pose_per_move: Setting to true will output a pose after each move/revert.
recover_lowest_assembly: Setting to true will output the lowest assembly in the final pose
recursive_depth: How many nodes after the terminal node should we keep track of alignments for?
pose_segment_starts: Residue numbers of the first residue in each segment in the input pose
pose_segment_ends: Residue numbers of the last residue in each segment in the input pose. Length must match that of pose_segment_starts.
pose_segment_dssp: String indicating the secondary structure of user-specified segments, one character per segment (e.g. HLH for a helix-loop-helix motif). Length should match that of pose_segment_starts and pose_segment_ends if specified.
strict_dssp_changes: Segments require at least a 2-residue change in DSSP to specify a new segment
set_segments_from_dssp: Determine segment boundaries based on pose secondary structure
match_segments: Which segments from the input pose should we be able to append onto? Defaults to exterior segments.
partner_pdb: Name of PDB file containing binding partner for this assembly
required_resnums: Residue numbers of residues in the input structure that must be preserved
max_recursion: How many alignments from the end nodes should be stored in memory?
modifiable_terminus: Which terminus of the starting node may be modified.
output_partner: Should the output pdb contain the partner?
extend_mode: Should SEWING append only a single helix?
start_node_vital_segments: Which segments from starting node are vital? (terminal or all)
required_selector: Residue selector specifying residues in the input structure that must be preserved. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
distance_cutoff: Cutoff for distance in Angstroms between segment and ligand to check for contacts
segment_distance_cutoff: Maximum number of segments away from the starting structure to look for contacts
binding_cycles: How many cycles to check for ligand contacts before giving up
build_site_only: Should we stop after finding all of the desired contacts?

Subtag AssemblyScorers: The subtags of this tag define the AssemblyScoreFunction that will be used to evaluate assemblies

Subtag InterModelMotifScorer: Basic Motif score among non-adjacent helices

weight: How heavily will this term be weighted during scoring?

Subtag IntraDesignTerminusMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?
optimum_distance: How far apart should that residue optimally be from the terminus?
maximum_unpenalized_variance: How far off from that can it be before it should be penalized?

Subtag LigandScorer: Scores how well ligand is buried based on orientation of nearby Ca's

weight: How heavily will this term be weighted during scoring?
ligand_interaction_cutoff_distance: The distance cutoff between ligand atom and c alpha that is considered an interaction.

Subtag MotifScorer: Basic Motif score among all helices

weight: How heavily will this term be weighted during scoring?

Subtag PartnerMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?

Subtag SegmentContactOrderScorer: Favors assemblies whose segments form contacts with segments distant in the assembly

weight: How heavily will this term be weighted during scoring?

Subtag StartingNodeMotifScorer: Specifically scores packing against the starting node

weight: How heavily will this term be weighted during scoring?

Subtag SubsetPartnerMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?
region_start: What is the first residue of the scored subset?
region_end: What is the last residue of the scored subset?

Subtag TerminusMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?
partner_residue: Which residue of the partner should this scorer calculate distance to?
optimum_distance: How far apart should that residue optimally be from the terminus?
maximum_unpenalized_variance: How far off from that can it be before it should be penalized?
terminus: Which terminus should be scored?

Subtag TopNMotifScorer: Basic Motif score among all helices

weight: How heavily will this term be weighted during scoring?
scores_to_keep: How many scores from each pair should be counted?

Subtag AssemblyRequirements: Subtags of this tag define the set of requirements that will be used when evaluating SEWING assemblies

Subtag ClashRequirement: Checks for clashes between segments in the assembly

maximum_clashes_allowed: Maximum number of clashes to allow in the assembly
clash_radius: Radius in Angstroms within which two residues are considered to be clashing

Subtag DsspSpecificLengthRequirement: Restricts the number of residues in segments with the specified DSSP

dssp_code: DSSP code whose length the requirement is restricting
maximum_length: Maximum number of residues in a segment with the given secondary structure
minimum_length: Minimum number of residues in a segment with the given secondary structure

Subtag KeepLigandContactsRequirement: Fails if an assembly's ligands lose more than a set number of contacts

contact_distance_cutoff: Maximum distance between two contact atoms before the contact is considered broken

Subtag LengthInResiduesRequirement: Checks the number of segments in the assembly

maximum_length: Maximum number of residues to allow in the assembly
minimum_length: Minimum number of residues in the final assembly

Subtag LigandClashRequirement: Checks for clashes between the assembly and its ligands

maximum_clashes_allowed: Maximum number of clashes to allow in the assembly
clash_radius: Radius in Angstroms within which two residues are considered to be clashing

Subtag SizeInSegmentsRequirement: Checks the number of segments in the assembly

maximum_size: Maximum number of secondary structure elements (including loops) to allow in the assembly
minimum_size: Minimum number of secondary structure elements (including loops) in the final assembly

Subtag Ligands: Subtags of this tag specify the ligands present in the input pose and their respective protein contacts.

Subtag Ligand: Specifies the position of a ligand and the contacts that it forms with the input pose

partner_ligand: Is this ligand found in the partner PDB?
pdb_conformers: Name of file containing a list of PDBs (or other Rosetta-compatible input files) containing alternate ligand conformations to sample
alignment_atoms: Comma-separated list of atom names to use when aligning ligand conformers to one another
auto_detect_contacts: Should we automatically detect contacts that are joined to the ligand by inter-residue chemical bonds?
ligand_resnum: Residue number of ligand in either PDB or Rosetta numbering
ligand_selector: Residue selector indicating ligand(s) covered in this tag. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.

Subtag Contact:

partner_contact: Does this tag specify a contact with the partner PDB?
contact_resnum: (REQUIRED) Number of residue participating in this contact in PDB or Rosetta numbering
ligand_atom_name: Rosetta name for the ligand atom participating in the contact
contact_atom_name: Rosetta name for the protein atom participating in the contact

Subtag Coordination: Contains subtags defining ideal coordination environments for atoms in the ligand

coordination_files: Comma-separated list of coordination file names for this ligand
geometry_score_threshold: Maximum score geometry score to allow when forming a contact

Subtag IdealContacts:

distance: (REQUIRED) Ideal distance between ligand and contact atom
angle: Ideal angle between this atom's contacts
dihedral_1: Ideal dihedral angle: contact_base - contact - ligand_atom - other_contact
dihedral_2: Ideal dihedral angle: contact - ligand_atom - other_contact - other_base
max_coordinating_atoms: (REQUIRED) Maximum number of contacts that this atom can form. Note that IdealContacts tags do not need to be defined for atoms with no contacts.
ligand_atom_name: (REQUIRED) Rosetta name of the ligand atom to which this tag applies

Defining the ligand coordination environment

The Coordination subtag of the Ligand tag (which is documented here), contains two types of ligand coordination information. First, it contains the "coordination_files" attribute, which provides a comma-separated list of all ligand coordination files (described below) that will be used to identify ligand contacts. Second, it provides information on each atom's preferred geometry in the form of IdealContacts subtags. Each ligand atom that will form new contacts will have its own IdealContacts subtag.

IdealContacts

Each atom's IdealContacts tag defines the atom name for which it should be applied, its preferred bond lengths ("distance"); bond angles about the atom ("angle"); and the ideal dihedral angles about the atom as defined in the XML schema above. Note that angles and dihedral angles will be accepted if they are any multiple of the entered value; for example, if the user requests a 90 degree angle, then bond angles of 180 degrees will also be accepted. The subtag also indicates the maximum number of contacts/bonds that the ligand should form, including existing contacts.

The final attribute of the IdealContacts tag, the geometry score threshold, indicates the tolerance that LigandBindingAssemblyMover should apply when scoring the geometry of newly added ligand contacts. This score is calculated as follows:

geometry_score = (delta_distance)^2 + 10*(mod(angle, ideal_angle))^2 + 5*(mod(dihedral_1, ideal_dihedral_1))^2 + 5*(mod(dihedral_2, ideal_dihedral_2))^2

Note that all angles are converted to radians for this calculation.

The recommended geometry score threshold will vary depending on the coordination environment of each ligand atom. For example, for a zinc ion with two initial contacts, a threshold of 5 provides the best balance of good geometry and high success rate for the addition of a third contact whereas a threshold of 20 provides the best results for a fourth contact.

Ligand Coordination Files

Please see the zinc_statistic_generator application documentation for more information on ligand coordination file generation.

The format for ligand coordination files can be found here.

Post-Processing

In many cases, users will want to add additional structural elements using AppendAssemblyMover after their ligands are fully coordinated. This can either be performed using a separate mover to allow for additional filtering/inspection beforehand or can be performed automatically within LigandBindingAssemblyMover by setting the "build_site_only" option to false. In this case, the min_cycles and max_cycles options would indicate the length of the AppendAssemblyMover run (whereas "binding_cycles" is used to determine the length of the LigandBindingAssemblyMover run), and the start_temperature and end_temperature options would control temperature ramping. This option is not recommended in most cases because AppendAssemblyMover will generally perform better with different add/delete probabilities and temperatures than LigandBindingAssemblyMover. For refinement after SEWING, please see the refinement of SEWING assemblies page.

Example

The following is an example RosettaScript using LigandBindingAssemblyMover:

<ROSETTASCRIPTS>
  <SCOREFXNS>
  </SCOREFXNS>
  <RESIDUE_SELECTORS>
    <ResidueName name="select_zn" residue_name3=" ZN" />
  </RESIDUE_SELECTORS>
  <FILTERS>
  </FILTERS>
  <MOVERS>
    <LigandBindingAssemblyMover name="assemble" binding_cycles="20000" model_file_name="/nas02/home/g/u/guffy/netscr/sewing_with_zinc/input_files/smotifs_H_5_40_L_1_6_H_5_40.segment\
s" add_probability="0.05" delete_probability="0.05" hashed="false" segment_distance_cutoff="2" distance_cutoff="8.0" start_temperature="2.0" build_site_only="true" window_width="4" \
>
      <Ligands>
        <Ligand ligand_selector="select_zn" auto_detect_contacts="true" >
          <Coordination coordination_files="/nas02/home/g/u/guffy/netscr/sewing_with_zinc/input_files/H_NEW_stats.txt" geometry_score_threshold="5" >
            <IdealContacts ligand_atom_name="ZN" max_coordinating_atoms="3" angle="109.5" distance="2.2" dihedral_1="30" dihedral_2="120" />
          </Coordination>
        </Ligand>
      </Ligands>
      <AssemblyRequirements>
        <DsspSpecificLengthRequirement dssp_code="L" maximum_length="6" /> Prevents super-long loops                                                                                  
        <DsspSpecificLengthRequirement dssp_code="H" minimum_length="10" /> Prevents super-short helices                                                                              
        <ClashRequirement />
        <SizeInSegmentsRequirement maximum_size="9" minimum_size="5" />
        <LigandClashRequirement />
      </AssemblyRequirements>
    </LigandBindingAssemblyMover>
  </MOVERS>
  <APPLY_TO_POSE>
  </APPLY_TO_POSE>
  <PROTOCOLS>
        <Add mover_name="assemble" />
  </PROTOCOLS>
</ROSETTASCRIPTS>

Guidelines for use

Since the sampling space of LigandBindingAssemblyMover is highly restricted, users are recommended to use relatively high temperature values (between 2.0 and 3.0) to ensure diverse sampling. Note that this mover does not perform temperature ramping; instead, the user-specified max_temperature sets the value for the entire protocol. LigandBindingAssemblyMover also ignores the min_cycles and max_cycles options; instead, the number of cycles is determined by the ligand_binding_cycles option. A value of 20000 cycles is recommended for adding a single ligand contact to ensure a high rate of success.

To prevent wasted sampling, users are recommended to use a segment distance cutoff of no more than two. Note that this cutoff counts the number of additions rather than the number of segments added, so segment files containing larger substructures may have different requirements. A max_distance of 8.0 Å is also recommended to prevent unnecessary calculations in segments that are not close enough to form contacts with the ligand. Recommended values for the user-specified geometry score threshold can vary significantly depending on the coordination environment of the specified atom. Lower scores generally indicate more ideal geometry (and therefore a stricter cutoff). Since these scores include angles and dihedrals between all pairs of contacts to the atom in question, the score scales nonlinearly with the number of contacts; for example, a value of 5.0 is appropriate for a tetrahedrally coordinated atom forming a third contact whereas a value of 20.0 will give similarly ideal geometries when forming a fourth contact. Deviations from ideal coordination geometry in the starting site can also lead to increased scores. Therefore, users are recommended to perform some benchmarking for their specific use case before performing full-scale simulations.