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KVFinder Manual In this documentation we are going to describe the basic and advanced features of KVFinder.
Basic This tab is destined for users willing to make a basic analysis of protein cavities. This option executes KVFinder prospecting the whole protein with a basic b asic set of options. This list defines which protein will be used as input. The list is generated using PyMOL's Input File – This active molecular objects. Refresh List – Refreshes Refreshes the list of objects on the input file selector. Run KVFinder – Executes Executes the basic mode. First it checks the consistency of KVFinder configurations (on the Configurations tab) and basic options. If any of these conditions fail, an appropriate warning message will be displayed. The output PDB file is loaded on the PyMOL viewer and output information are displayed on the Results tab. Basic Options – These These are the entry parameters which define KVFinder on the basic mode. KVFinder defines a grid on the search space, which in the basic mode is the whole protein. Step Size – KVFinder The step size is the distance between grid points, this parameters directly affects KVFinder precision. The relationship between search space size and step size defines the number of points on the grid, thus affecting execution time. Inner Probe and Outer Probe Size - KVFinder works with a two sized probe system to find open cavities. A smaller probe, dubbed Probe In, and a bigger one, the Probe Out, roll around the protein. The points reached by the Probe In but not by the Probe Out are considered cavity points. Depending on the characteristics of the studied cavity, the user might want to adjust the probes size. Minimum Cavity Volume – Sets a filter on the KVFinder output, excluding cavities with smaller volumes than this parameter. Output Base Name – KVFinder generates as output PDB file and a results text file containing information about the cavities found. This entry field defines the prefix name of the output files. Overwrite Existing File – To To avoid data loss, the software prevents the user to generate an output file with the same name of a PyMOL active object. If this option is checked, this verification will not be made, and previous objects with the same name will be overwritten. Advanced This tab features KVFinder execution with a complete set of options, defined by the Options sub section. Draw New Box - This feature creates a box around a user defined search space – (sele). (sele). If there is
already a box, it will be deleted and replaced by the new one. Delete Box - Deletes the previous box from PyMOL viewer. Box-Padding – Defines Defines padding around the selection which the box will be created. KVFinder Manual
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Minimum/Maximum slides – These slides can be used to adjust the box size. Each axis is identified
by a color. The base reference of the box is the vertex where the colored edges meet. Minimum slides move the edge next to the base, while maximum slides control the opposite side of the edge. Angle slides – Rotates the box. Input File – This list defines the protein target that will be used as input. The list is generated using PyMOL's active molecular objects. Refresh List – Refreshes the list of objects on the input file selector. Output Folder – All files generated by KVFinder will be saved on this specified folder. Output Base Name – KVFinder generates as output PDB file and a results text file containing information about the cavities found. This entry field defines the prefix name of the output files. Overwrite Existing File – To avoid data loss, the software prevents the user to generate an output file with the same name of a PyMOL active object. If this option is checked, this verification will not be made, and previous objects with the same name will be overwritten. Run KVFinder - Executes the advanced mode. First it checks the consistency of KVFinder configurations (on the Configurations tab) and options. If any of these conditions fail, an appropriate warning message will be displayed. The output PDB file is loaded on the PyMOL viewer and output information are displayed on the Results tab. Save Parameters - Saves a Parameters file with the set configurations without running KVFinder. This file can be used as base parameters file for command line execution. Advance Options This tab contains some of KVFinder's main features. The set of options defined here are passed as parameters for KVFinder on advanced mode. Step Size – KVFinder defines a grid on the search space. The step size is the distance between grid
points, this parameters directly affects KVFinder precision. The relationship between search space size and step size defines the number of points on the grid, thus affecting execution time. Probe In Size and Probe Out Size - KVFinder works with a two sized probe system to find open cavities. A smaller probe, dubbed Probe In, and a bigger one, the Probe Out, rolls around the protein The points reached by the Probe In but not by the Probe Out are considered cavity points. Depending on the characteristics of the studied cavity, the user might want to adjust the probes size. Minimum Cavity Volume – Sets a filter on the KVFinder output, excluding cavities with smaller volumes than this parameter. Useful to exclude uninteresting cavities from the output. Probe Out Adjustment – This is the default operation mode, the double probe system, restricted to a user defined search space. Whole Protein – Defines the search space as the whole protein. NOTE – If none of the above options is selected, KVFinder will use only the small probe to define cavities. It may be useful for quicker and detailed analysis of closed cavities, as the probe out won't affect it's results. Another possibility is using it to achieve better results of surface area on open cavities or small molecules, but in these cases, the volume calculated isn't reliable. Surface – Selects surface type to be considered, Solvent Accessible Surface (SAS) or Molecular KVFinder Manual
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Surface (VdW). Step Redimensioning – If this option is set, the maximum number of points on the KVFinder grid will
be limited. The number of points on the grid is a relation between the search space size and grid step size. The grid step will be increased to an acceptable value if the number of points of the defined grid exceeds the limit. This option prevents the user from experiencing extremely long analysis time, but it may be set off for better results, when a more detailed analysis is needed. Ligand Adjustment – This option is used when the user wants to limit the search space around a ligand. The ligand is set in the Ligand Filename selector, while the radius of the search is defined by the Distance Cutoff (Å) entry. Ligand Filename – Defines the ligand target for the adjustment. It may be a PyMOL object or a PDB file. Refresh List – Refreshes the list of structures to be used as targets on the Ligand Adjustment mode. It uses the list of active objects on PyMOL. Another File – Gives the user the option of selecting a PDB file as ligand to be used on the Ligand Adjustment mode. Distance Cutoff – Defines the search radius (Å) of the Ligand Adjustment mode. Restore Default Values – Restores the initial values of the Advanced - Options tab. Results This tabs displays KVFinder results. On the top of the tab, basic information about the execution are displayed (Input File, Output File and Ligand Adjustment File used, if any). KVFinder Output - Volume and Area – Displays the calculated volume for each cavity, identified by a three letter code. If the user selects a cavity in any of these output lists, an active object is created for visual inspection. Load Results – Loads a KVFinder results file, loading the input and output PDB files. Also loads the cavities information on the interface. Residues Around – Selecting a cavity on this list creates an active object containing only the protein residues that are in contact with the selected cavities. Configurations On this tab, it is possible to define file containing basic data used by KVFinder, giving the user a chance to personalize the analysis. The dictionary file contains the Van der Waals Radii for atoms of the recognized residues. This file has a mandatory format:
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--------------------------------------------------------------------#all line starter with # is ignored by KVFinder #(3 letters residue name) >ALA #Atom_name Radius N 1.8240 H 0.6000 HB1 1.4870 >ARG CB HB2 2HB
1.9080 1.4870 1.4870
>GEN #(when an atom is not founded in a specific residue KVFinder use a generic value of the radius for the atom) AC 2.00 AG 1.72 AL 2.00 ---------------------------------------------------------------------
Command Line KVFinder is also available as a command line executable, dubbed kvfinder on Linux or kvfinder_win on windows. All adjustable parameters can be set through command line arguments. -h - Show all the possible arguments and a tiny description of it -i - Defines an input PDB to be prospected. If a parameters file is not provided, a whole protein prospection with the default configurations will be made. The output file will have a reference to the input file name. -l - A text file containing a list of PDBs to be prospected. All of them will be executed with the same set of parameters. As stated above, if no parameters file is provided, the whole protein with default settings will be prospected. The output will have a reference to the input files. -p - Defines a Parameters File to be used as reference. If advanced configurations will be used on KVFinder run, the user can generate a Parameters file (KVFParameters), with the desired configuration, setting for example the search space using the box, through the graphical interface, and use this on one or several PDB files on the command line mode. Configurations made on the command line overwrite configurations of the Parameters file. -g - Set the grid spacing to be used. -r - Define the radius of the smaller probe. -t - Defines the radius of the bigger probe. -v - Defines a volume threshold, to filter noise cavities. KVFinder Manual
