Overview

The Guided Ligand Replacement (GLR) module is intended to facilitate ligand placement when the X-ray crystal structure of at least one similar protein:ligand complex is known. GLR is often employed in structure-assisted drug design where the structures of many related protein:inhibitor complexes are determined. It is especially useful for complicated ligands and when there are multiple independent copies in the asymmetric unit.

The Guided Ligand Replacement (GLR) tool is designed to use prior knowledge from a previously fit ligand to expedite the fitting of a "similar" ligand into the same or "similar" protein. The similarity required between the pair of ligands can be as little as a few atoms.

The proteins are overlayed using phenix.superpose_pdbs. The ligands are matched using the electronic Ligand Builder and Optimization Workbench (eLBOW) via another tool called phenix.superpose_ligands. Once the ligand has been fit, a Real-Space Refinement (RSR) is performed and the final model written to disk.

Usage

Usage

phenix.guided_ligand_replacement [options] \
  target_pdb_file_name=structure-in-which-target-ligand-is-to-be-placed.pdb \
  ligand_cif_file_name=parameterization-of-target-ligand.cif \
  map_coeffs_file_name=map-coefficients-for-target-electron-density.mtz \
  guide_pdb_file_name=structure-of-reference-protein-ligand-complex.pdb \
  ligand_selection_in_guide_model=selection-to-identify-reference-ligand \
  replace_ligand_in_guide_pdb_file_name=[true|false]

Input files

GLR requires a number of inputs and also has some options, all of which are provided using the phil formalism. The list of inputs:

• guide_pdb_file_name: Name of the PDB file for the structure of the reference protein:ligand complex. While the protein used in the target and reference structures is usually the same, the protein sequences need only be sufficiently similar to reliably superimpose.
• protein_pdb_file_name: Name of PDB file in which the target (i.e. new) ligand is to be placed. This structure is typically the apo structure from molecular replacement after one round of refinement.
• map_coeffs_file_name: Name of the map coefficient file for the electron density in which the target ligand is to be placed. This file is typically the MTZ file from latest run of phenix.refine. If this file contains more than one set of possible map coefficients, the first recognized set is used. If structure factors are provided (e.g. MTZ file with only FOBS and SIGFOBS), the 2Fo-Fc map is calculated and used. Map files (e.g. .map) are used directly.

The input for the ligand can be any input file that is readable by eLBOW. Either or both of the following phil parameters can be used.

• ligand_input_file_name: this is a file containing chemical information about the ligand.
• ligand_cif_file_name: this is the of a ligand restraints file for the RSR step. If not supplied, the restraints are generated from ligand_input_file_name.
• ligand_code: the ligand code from the PDB Chemical Components so that restraints and geometry can be generated.

Optional inputs include:

• ligand_selection_in_guide_model: Standard PHENIX selection expression to identify the reference ligand in the reference structure. A typical selection might look like "resname LG1 and resid 1". While GLR tries to make a sensible selection based on ligand code or uniqueness, it may be necessary to make an explicit selection.

• replace_ligand_in_guide_pdb_file_name=[true|false]: By default, this parameter is set to false and can be omitted. If this parameter is set to true, the reference structure is also used as the target structure (protein_pdb_file_name parameter is ignored). This functionality is useful in two circumstances:

  1) the first copy of the ligand is placed manually and it needs
  to be propagated throughout the asymmetric unit
  
  2) the current ligand is incorrect (e.g. GTP instead of ATP) or
  needs to be updated (e.g. remove non-standard atom names).
  

• phenix.superpose_pdbs: this allows selection of the same parameters as in the standalone program.

Output files

By default, GLR will generate a PDB file with the fit ligand.

Examples

phenix.guided_ligand_replacement \
  target_pdb_file_name=3KQC-apo.pdb \
  ligand_cif_file_name=LGK.cif \
  map_coeffs_file_name=refine-apo.mtz \
  guide_pdb_file_name=3KQE.pdb \
  ligand_selection_in_guide_model="resname LGM"

phenix.guided_ligand_replacement < glr.phil > glr.log

References

• Ligand placement based on prior structures: the guided ligand-replacement method. H.E. Klei, N.W. Moriarty, N. Echols, T.C. Terwilliger, E.T. Baldwin, M. Pokross, S. Posy, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 70, 134-43 (2014).

• electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. N.W. Moriarty, R.W. Grosse-Kunstleve, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 65, 1074-80 (2009).

List of all available keywords

• guided_ligand_replacement
  • job_title = None Job title in PHENIX GUI, not used on command line
  • input
    • guide_pdb_file_name = None PDB filename containing protein model and docked ligand that can guide the placement of new ligand into the an apo model
    • protein_pdb_file_name = None PDB file containing protein into which the ligand will be fit.
    • ligand_input_file_name = None File containing chemical input of a ligand
    • ligand_code = None Ligand code from Chemical Components
    • data_file_name = None Amplitudes or intensities
    • map_coeffs_file_name = None Map coefficients from a refinement of the apo model
    • ligand_cif_file_name = None This restraints file will be used for the real space refinement. If not suplied, a set of restraints are generated from the ligand input.
    • ligand_selection_in_guide_model = None The specific ligand to use from the guide structure, using the standard Phenix atom selection syntax.
    • real_space_refinement = *ideal off Perform a real space refinement after each ligand is added
    • real_space_refinement_selection_radius = 5.
    • replace_ligand_in_guide_pdb_file_name = False Use this option to replace the ligand in the Guide protein. This option saves creating a apo model of the same protein.
    • map_labels = None
  • output
    • file_name = None Defaults to current directory
    • job_title = None Job title in PHENIX GUI, not used on command line
  • superpose_pdbs
    • input
      • pdb_file_name_protein = None Name of PDB file with model to fit to
      • pdb_file_name_guide = None Name of PDB file with model that will be fit to pdb_file_name_protein
    • alignmentSet of parameters for sequence alignment. Defaults are good for most of cases
      • alignment_style = local *global
      • gap_opening_penalty = 1
      • gap_extension_penalty = 1
      • similarity_matrix = blosum50 dayhoff *identity
    • validation
      • rmsd_cutoff = 2.
      • similarity_cutoff = 80.
  • automatic_guidance
    • use_web_services = False Use the homology search in RCSB web services to identify and download candidate guide models.
    • use_local_directory = None A directory containing models to search for similar proteins to use as a guide for fitting a similar ligand, similarly bound.
    • minimum_ligand_similarity_tanimoto = 0.7 Minimum Tanimoto score to filter possible guide models.
  • process_control
    • nproc = 1
  • superpose_ligands
    • quick = True