OEBio Examples Summary

Molecule processing

Extract the backbone of a protein

A program that extracts the backbone from a protein. An example command would be:

backbone input.pdb output.pdb

See also

Split a Macro-molecular Complex

A program that splits components of a protein structure, returning separate ligand, protein-complex, waters, and other molecules.

An example command that limits the protein-complex output to just the binding site residues would be:

splitmolcomplex -separateresidues input.pdb output.oeb.gz

Help is available for all the supported OESplitMolComplexOptions parameters:

splitmolcomplex --help all
Complete parameter list
 Display options :
   -verbose : If true, return more verbose output

 SplitMolComplex options :
   -bindingsitenum : Select this binding site
   -covalentbondtreatment : Covalent bond treatment
   -covalentligand : Split covalent ligands
   -ligandfilter : Ligand filter category
   -ligandname : Ligand name
   -maxsitedistance : Maximum distance to be associated with the binding site
   -maxsurfacedistance : Maximum distance to be associated with the protein
                         surface
   -modelnum : Select this NMR model number
   -proteinfilter : Protein filter category
   -separateresidues : Separate individual residues before selection
   -surfacewaters : Select surface waters
   -waterfilter : Water filter category

 input/output options :
   -in : Input molecule (usually a pdb file)
   -out : Output molecule (usually an oeb)

Splitting a Macro-molecular Complex Efficiently and Flexibly

A program that splits components of a protein structure, returning separate ligand, protein-complex, waters, and other molecules. This version uses the low-level API to fragment and then combine selected components.

An example command that limits the protein-complex output to just the binding site residues would be:

splitmolcomplexlowlevel -separateresidues input.pdb output.oeb.gz

Help is available for all the supported OESplitMolComplexOptions parameters:

splitmolcomplexlowlevel --help all
splitmolcomplexlowlevel <inmol> [<outmol>]
Complete parameter list
    Display options :
      -verbose : If true, show molecule titles and number of binding sites

    SplitMolComplex options :
      -bindingsitenum : Select this binding site
      -covalentbondtreatment : Covalent bond treatment
      -covalentcofactor : Split covalent cofactors
      -covalentligand : Split covalent ligands
      -ligandfilter : Ligand filter category
      -ligandname : Ligand name
      -maxsitedistance : Maximum distance to be associated with the binding site
      -maxsurfacedistance : Maximum distance to be associated with the protein
                            surface
      -modelnum : Select this NMR model number
      -proteinfilter : Protein filter category
      -separateresidues : Separate individual residues before selection
      -surfacewaters : Select surface waters
      -waterfilter : Water filter category

    input/output options :
      -in : Input molecule (usually a pdb file)
      -out : Output molecule (usually an oeb)

Split a Macro-molecular Complex Into Fragments

A program that extracts and filters components of a protein structure, returning individual fragments.

An example command that returns just the ligands for all binding sites would be:

splitmolcomplexfrags -waterfilter nothing -proteinfilter nothing -bindingsitenum 0 input.pdb output.sdf

Help is available for all the supported OESplitMolComplexOptions parameters:

splitmolcomplexfrags --help all
Complete parameter list
 Display options :
   -verbose : If true, return more verbose output

 SplitMolComplex options :
   -bindingsitenum : Select this binding site
   -covalentbondtreatment : Covalent bond treatment
   -covalentligand : Split covalent ligands
   -ligandfilter : Ligand filter category
   -ligandname : Ligand name
   -maxsitedistance : Maximum distance to be associated with the binding site
   -maxsurfacedistance : Maximum distance to be associated with the protein
                         surface
   -modelnum : Select this NMR model number
   -proteinfilter : Protein filter category
   -separateresidues : Separate individual residues before selection
   -surfacewaters : Select surface waters
   -waterfilter : Water filter category

 input/output options :
   -in : Input molecule (usually a pdb file)
   -out : Output molecule (usually an oeb)

Preparing a Protein

A program that selects the highest occupancy alternate locations of a protein, adds hydrogens in orientations that make appropriate hydrogen bonds, and splits out the complex for the selected binding site (optionally separating the ligand from the protein complex). This is an initial prototype of a “protein prep” workflow.

An example command that splits out the ligand and limits water sampling is as follows:

proteinprep -waterprocessing ignore input.pdb prot.oeb.gz lig.oeb.gz

Help is available for all the supported parameters:

proteinprep --help all
proteinprep [-options] <inmol> [<outcplx> [<outlig>]]
Complete parameter list
    SplitMolComplex options :
      -bindingsitenum : Select this binding site
      -covalentligand : Split covalent ligands
      -ligandfilter : Ligand filter category
      -ligandname : Ligand name
      -maxsitedistance : Maximum distance to be associated with the binding site
      -maxsurfacedistance : Maximum distance to be associated with the protein
                            surface
      -modelnum : Select this NMR model number
      -proteinfilter : Protein filter category
      -separateresidues : Separate individual residues before selection
      -surfacewaters : Select surface waters
      -waterfilter : Water filter category

    input/output options :
      -in : Input molecule filename (must have 3D coordinates)
      -cplxout : Output complex filename
      -ligout : Output ligand filename

    Calculation options :
      -alts : Alternate location atom handling (affects atom:atom interactions)
      -placehydrogens : If false, hydrogens will not be added
      -waterprocessing : How waters are processed (can greatly affect runtime)
      -standardizehyd : If false, bonds for hydrogens are not adjusted to standard
                      lengths
      -clashcutoff : Van der Waals overlap (in Angstroms) defined to be a bad
                     clash
      -flipbias : Scale factor for the bias against flipping sidechains such as
                  HIS

    Display options :
      -verbose : Display more information about the process

Protein-Ligand Interactions

Perceive and Print Protein-Ligand Interactions

The program that perceives protein-ligand interactions and prints them out.

An example command would be:

printinteractions complex.pdb

Help is available for all the supported OESplitMolComplexOptions parameters:

printInteractions --help all
Simple parameter list
   SplitMolComplex options :
     -ligandname : Ligand name

   input/output options :
     -complex : Input filename of the protein complex