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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 set of options.
Input File This list defines which protein 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.
Run KVFinder 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 are the entry parameters which define KVFinder on the basic mode.
Step Size KVFinder defines a grid on the search space, which in the basic mode is the whole protein.
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 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). 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 padding around the selection which the box will be created.
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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
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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 () 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 () 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