In contrast to Docking applications DisVis is aimed at explorative modeling, i.e. checking
data-consistency and information content of distance restraints intented to directly design
follow up studies or to generate a filtered restraint set to drive molecular Docking
e.g. with HADDOCK.
A typical DisVis investigation thus should start with determining the consistency of the
restraints dataset using the “quick scanning” option. After inspecting the results, the
dataset can be filtered to discard false-positive restraints using the violation analysis.
When the consistency of the dataset has been secured, additional runs can be performed with
the “complete scanning” setting and optionally targeted interface analysis.
With the resulting information, interface residues can be inferred and through the
occupancy analysis the putative binding pose of the ligand can be approximated.
These insights are of use in determining future experiments to further characterize the
interaction.
Input
Fixed chain:
a file in pdb or mmCIF format containing the coordinates of the fixed chain which will be kept stationary
during the search of the accessible interaction space.
Scanning chain:
a file in pdb or mmCIF format containing the coordinates of the scanning chain which will be moved
during the search of the accessible interaction space.
NOTE: Selecting the smaller interaction partner as scanning chain
speeds up the calculation. However, the density map of the accessible interaction space is
only provided for the fixed chain.
Restrains file:
a text-file containing the distance restraints in the following format:
First selection (here "A 18 CA") must correspond to the fixed chain and the second selection (here "F 27 CB") the scanning chain.
This puts a distance restraint between the CA-atom of residue 18 of chain A of the fixed chain and the
CB-atom of residue 27 of chain F of the scanning chain that should be longer than or equal to 10A and
smaller than or equal to 20A.
Comments can be added by starting the line with the pound sign (#) while empty lines are ignored.
Interaction analysis (Residue selection):
The interaction analysis can be performed to determine which residues are most likely at the interface.
For this a a plain text file needs to be provided specifying the residue numbers of the fixed
and scanning chain for which the interaction analysis should be performed. The input file
consists of two lines, where the two lines are a space separated sequence of residue numbers
with the first line corresponding to the fixed chain and the second line corresponding to
the scanning chain. As the interaction analysis is particularly expensive, only complexes
consistent with all-3 up to all restraints are considered. NOTE: It is advised to perform a "quick scanning" without the interface analysis first
to ascertain that complexes consistent with all-3 restraints exist.
A simple example for the selection-file:
1 2 3 4
101 302 888
This will select residue numbers 1, 2, 3, and 4 for the fixed and 101, 302, and 888 for the
scanning chain.
Occupancy analysis:
It is possible to perform a grid occupancy analysis for complexes consistent with
all-3 up to all number of restraints by activationg this option on the
submission page. This will produce a density map in the coordinate space of the fixed
chain giving a normalized indication of how frequent a grid point is occupied by any
atom of the scanning chain.
Tag:
A custom tag to identify your run. Supported characters: a-z A-Z 0-9 _ + - = / , . :
Parameters:
Rotational sampling interval - Rotational sampling density in degrees
Voxel spacing - Voxel spacing of search grid in angstrom
Interaction radius - Radius of the interaction space for each
atom in angstrom. Atoms are thus considered interacting if the distance is larger than
the vdW radius and shorther than or equal to vdW + interaction_radius
Maximum clash volume - Maximum allowed volume of clashes.
Increasing this number results in more allowed complexes.
Minimum interaction volume - Minimal required interaction volume
for a conformation to be considered a complex. Increasing this number results in a stricter
counting of complexes.
Output
accessible_complexes.out:
a text file containing the number of complexes consistent with a given number of restraints.
Column 1 shows the number of consistent restraints for each complex counted, denoted by N;
column 2 shows the number of complexes consistent with exactly N restraints; column 3 shows
the fraction of all complexes sampled that are consistent with exactly N restraints; column 4
gives the number of complexes consistent with at least N restraints, and is thus the cumulative
sum of column 2; column 5 is again the fraction of complexes consistent with at least N restraints,
and also the cumulative sum of column 3.
violations.out:
a text file showing how often a specific restraint is violated for complexes consistent with
a number of restraints. The higher the violation fraction of a specific restraint, the more
likely it is to be a false-positive. Column 1 shows the number of consistent restraints N,
while each following column indicates the violation fractions of a specific restraint for
complexes consistent with at least N restraints. Each row thus represents the fraction of all
complexes consistent with at least N restraints that violated a particular restraint.
accessible_interaction_space.mrc:
a density file in MRC format. The density represents the center of mass of the scanning chain
conforming to the maximum found consistent restraints at every position in space. The density
can be inspected by opening it together with the fixed chain in a molecular viewer.
z-score.out:
a text file giving the z-score for each restraint. The higher the score, the more likely the
restraint is a false-positive. Z-scores above 1.0 are explicitly mentioned in the output.
The first column indicates the restraint; column 2 gives the average violation fraction, i.e.
the average of the corresponding column in violations.out; column 3 represents the standard
deviation of the average violation fraction; and column 4 finally gives the z-score.
disvis.log:
a log file showing all the parameters used, together with date and time indications.
If an occupancy and/or interaction analysis was requested, disvis also outputs the following files:
occupancy_N.mrc:
a volume file giving a normalized indication of how frequent a grid point is occupied by
the ligand, where N indicates the minimal required number of consistent restraints that
resulted in the occupancy grid.
[receptor|ligand]_interactions.txt:
a text file containing the average number of interactions per complex for each selected
residue made, for both the fixed (receptor) and scanning chain (ligand).
Each column denotes the minimal number of consistent restraints of each complex for
which interactions were counted.
Visualizing the accessible interaction space/occupancy analysis
The accessible interaction space consistent with at least N restraints as well as the density
maps of the occupancy analysis can be visualized by
opening the fixed chain (fixed_chain.pdb) used in the disvis run together with the
accessible_interaction_space.mrc/occupancy_N.mrc output file with
UCSF Chimera.
The density slider in Chimera can be adjusted to change N.
Help/Contact
If you have further questions or run into issues submitting your data, please contact us at
disvis.server[at]gmail.com.