SPRUCE - Protein Preparation from PDB Codes¶
This floe uses Spruce to prepare biomolecules for downstream modeling applications in Orion, such as docking, posit, gameplan, or short-trajectory MD.
The required input for this floe is PDB codes. The PDB (or MMCIF if the PDB is not available), as well as the MTZ file, containing the electron density maps, (if available) will be downloaded from the RCSB.
An additional input dataset from a previous Classic Spruce: Prep run may be used as a reference for biological unit extraction and superposition to a common reference frame.
If a ligand cannot be detected during the run, consider specifying the ligand residue name, increasing the size of the input variable “max_residues”, given as an optional input to this floe. Or if this is a known apo structure, you can provide the definition of a residue in the binding site.
You can read more about Spruce in the toolkit documentation.
Extra Required Parameters
Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field Include density based depictions (boolean) : Include density based depictions.Default: True Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field Output Dataset (dataset_out) : Output dataset to write toDefault: Failed_Spruce_prep_dataset Output Dataset (dataset_out) : Output dataset to write toDefault: Spruce_prep_dataset Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field Components to be part of the molecule (string) : Components to make part of the molecule.If set to ‘undefined’, will not be included in outputDefault: [‘protein’]Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors Discard liganded design units (boolean) : Option to discard liganded design units.Default: True Generate surface (boolean) : Option to generate surface for pockets.Default: True Local burial factor (decimal) : Option to set local burial factor.Default: 1.4 Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field Max surface area (decimal) : Option to set maximum surface area for pocket finding.Default: 3000.0 Min surface area (decimal) : Option to set minimum surface area for pocket finding.Default: 150.0 Add interaction hints (boolean) : Option add interactions to the design units.Default: True Add style (boolean) : Option add style to the design units.Default: True Allow cap residue truncation (boolean) : Option to allow terminal residue to converted to cap, if cap will otherwise clash.Default: True Alternate location handling method (string) : Option to pick method of handling alternate locations.Default: DefaultChoices: Primary, Enumerate, Default Loop backbone clash threshold (decimal) : Loops from the database where more than the threshold fraction of the backbone atoms clash, are rejected.Default: 0.25 Build C-terminal caps (boolean) : Option to cap broken C-termini in protein chains.Default: True Option to build disulfide bridges (boolean) : Allow the loop builder to build disulfide bridges during loop modeling (if possible).Default: True Build missing loops (boolean) : Option to build missing loops (if information is available to do so)Default: True Build N-terminal caps (boolean) : Option to cap broken N-termini in protein chains.Default: True Build partial sidechains (boolean) : Option to build missing or partial protein sidechains.Default: True Build missing tails (boolean) : Option to build missing tails (if information is available to do so)Default: False Loop builder include crystal packing (boolean) : Include packing residues when building loops.Default: False Assign charges and radii (boolean) : Option to assign partial charge and radii.Default: True Collapse non-site alts (boolean) : Option to deduplicate structures with different alts, if the alt locations are not near the binding site.Default: True Loop crop length (integer) : Anchor residues on the protein to crop back for a better fit, results in longer loops being built.Default: 1 Delete clashing solvent (boolean) : Option to allow build steps to remove clashing solvent.Default: True Duplicate removal (boolean) : Option to deduplicate identical structures resulting from symmetry operation.Default: True Enumerate co-factor sites (boolean) : Option to generate individual design units based on the recognized co-factors.Default: False Enumerate pockets (boolean) : Option to enumerate pockets when no ligand is foundDefault: False Fix backbone atom issues (boolean) : Option to fix backbone atom issues in protein chains.Default: True Generate Tautomers (boolean) : Option to generate and use tautomers in the hydrogen network optimization.Default: True Hetgroup cluster distance (decimal) : Distance between heterogens used to determine optimization clusters for protonation.Default: 3.5 Include SA term (boolean) : Include solvent accessible surface area term when ranking the loops.Default: True Include solvation (boolean) : Include simple solvation model when building loops.Default: True Include Binding Site Grids (boolean) : Include electron density and difference density maps around the binding siteDefault: True Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field Loop clash threshold (decimal) : Loops from the database where more than the threshold fraction of the loops atoms in addition to the bacbkone clashing ones clash, are rejected.Default: 0.2 Loop anchor atom distance buffer (decimal) : Fuzzy matches in the loop database has to have distance between anchor atoms correct, +/- buffer distance.Default: 1.0 Make packing residues (boolean) : Generate packing residues from an asymmetric unit.Default: True Maximum atoms in biological unit (integer) : Option to limit the size of BUs processed based on number of atoms.Default: 50000 Maximum parts in biological unit (integer) : Option to limit the size of BUs processed based on number of parts (chains).Default: 24 Number of loops to minimize and evaluate (integer) : Maximum number of loops to connect and minimize.Default: 5 Max atoms for a ligand (integer) : Maximum number of atoms in a molecule to be detected as a ligand. For peptides we recommend 200Default: 100 Max residues for a ligand (integer) : Maximum number of residues in a molecule to be detected as a ligand. For peptides we recommend 20Default: 5 Max system atoms (integer) : Maximum number of atoms in the system.Default: 50000 Minimum alignment score for BU extraction (integer) : Option to specify minimum sequence alignment score for biounit extraction.Default: 200 Min atoms for a ligand (integer) : Minimum number of atoms in a molecule to be detected as a ligand. For fragments we recommend setting to 5Default: 8 Optimize Experimental Protons (boolean) : Option to optimize hydrogens assigned in the experiment.Default: False Loop optimization shell (decimal) : Include atoms within this distance in the loop optimization, larger distance results in slower optimizations.Default: 15.0 Opt stage 1 step/residue multiplier (integer) : Number of steps per number of residues in the loop for the first stage optimizer.Default: 5 Opt stage 2 step/residue multiplier (integer) : Number of steps per number of residues in the loop for the second stage optimizer.Default: 10 Loop optimization tolerance (decimal) : Tolerance for the loop optimization, smaller numbers result in slower optimizations.Default: 0.001 Output BioDesignUnits (boolean) : Option to write intermediate work produce bio design unitsDefault: False Prefer author BIOMT records (boolean) : Option where the author BIOMT record is prefered over the software generated one.Default: True Protonate (boolean) : Option to add and optimize protons in the system.Default: True Restrict DUs to ref site removal (boolean) : Option to not generate design units with sites not matching the reference (if one is provided).Default: True Rotamer Coverage % (decimal) : Coverage of the rotamers returned from the library in percent.Default: 100.0 Rotamer Library (string) : Rotamer library to use for side-chain building.Default: Richardson2016Choices: Dunbrack, Richardson, Richardson2016 Size used to define binding site (decimal) : Distance used to determine the size of the site.Default: 5.0 Strict Ligand (boolean) : Option to only emit design units with ligands that match the ligand names (if any are provided)Default: True Enforce proline positions in loop templates (boolean) : Fuzzy matches in the loop database have to have proline in exact locations of sequence.Default: True Strict protonation mode (boolean) : Option to fail prep if protons could not be added.Default: False Superpose design units (boolean) : Option to superpose DUs (if multiple), first onto the reference structure (if provided).Default: True Superposition method (string) : Superposition method.Default: SiteSequenceChoices: GlobalSequence, SiteSequence, DDMatrix, SSE, SiteHopper Target classication (string) : Option to pick whether target is protein or nucleic acid component.Default: ProteinChoices: Protein, Nucleic Number to transform (integer) : Number of loops to allow through the sidechain clash checker. No matter this number, will process all with an identical sequence to target.Default: 25 Codes delimiter (string) : Delimiter to separate multiple PDB codes.Default: , PDB code(s) to download (string) : Separate multiple codes with a (default) comma delimiter, e.g. ‘1ABC, DEF2, G3HI’. Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field Download timeout (integer) : Timeout when attempting to download files for each PDB code.Default: 600