The example directory contains examples for the two variants of the
protocol: 1) SnugDock alone contained in the "SnugDock" directory and,
2) EnsembleDock and SnugDock combination protocol contained in the
"EnsembleDock_plus_SnugDock" directory.

Note: All directories paths are in reference to the "example"
directory root.

A) Preparing the environment

1) Paths: Prior to launching any executable, you have to ensure that the paths
of the executable and the input and the output directories match your
directory structure. The paths file in the following places need to be
modified to match your paths:
i) SnugDock/prepack/paths.txt
ii) SnugDock/SnugDock/paths.txt
iii) EnsembleDock_plus_SnugDock/prepack/paths.txt
iv) EnsembleDock_plus_SnugDock/EnsembleDock_plus_SnugDock/paths.txt

2) If a native structure is not present: Please remove the flag
   "-native 1vfb" from all the bash files:
i) SnugDock/prepack/prepack.bash
ii) SnugDock/SnugDock/SnugDock.bash
iii) EnsembleDock_plus_SnugDock/prepack/prepack.bash
iv) EnsembleDock_plus_SnugDock/EnsembleDock_plus_SnugDock/EnsembleDock_plus_SnugDock.bash



B) The Actual Runs
The docking simulations follow the general RosettaDock methodology of
an initial prepack stage where the side-chain rotameric states are
optimized followed by the actual docking step.

1) SnugDock only protocol: Directory "SnugDock"
All the inputs are contained in the subdirectory
"SnugDock/input/prepack_input". It contains the following files:
1vfb.pdb: The native pdb if available
FR02.fab: The FAb constraints file similar to that when using
RosettaDock with antibody. This helps in biasing the simulation
towards interfaces containing the CDRs.
FR02.pdb: The input structure
FR02.unbound.pdb: The structure from which side-chain rotameric states
are appended to the standard Dunbrak rotamers. If an unbound is not
provided, the rotamers of the input structure are lost.

Prepack:
a) Preparing the input: Prior to running the prepack, the subdirectory
"SnugDock/input" is supposed to be empty, (It is full because in the example
prepack has already run) and one has to copy over the contents of the
"SnugDock/input/prepack_input" to "SnugDock/input".
b) Lauching prepack: Enter the directory "SnugDock/prepack" and
execute the following command "./prepack.bash | tee prepack.logfile" (
The portion after the pipe is optional, and is needed if you want to
store the logfile of the prepack run )
c) Post processing the prepack output: After step (b) completes, go to
the directory "SnugDock/input" and rename the file "aaFR02_0001.pdb"
to FR02.ppk.pdb, and delete the prepack scorefile aaFR02.fasc. (For
reference the unmodified prepack output can be found here
"SnugDock/input/prepack_output"

SnugDock (only) run:
a) Preparing the input: In the directory "SnugDock/SnugDock", change
the "SnugDock.bash" file such that nstruct is 1000 (currently it is
10). Depending on the type of search (global/local), standard
RosettaDock command line flags can be used.
b) Lauching SnugDock: Execute the following command "./SnugDock.bash |
tee SnugDock.logfile". The portion after the pipe is optional, and is
needed if you want to store the logfile of the SnugDock run. )
c) Outputs: Depending on the nstruct value, you will have a
corresponding number of output structures in the directory
"SnugDock/SnugDock" named aaFR02_0001.pdb .... aaFR02_1000.pdb. ( in
this example there will be only 10 structures) A fullatom score file,
"aaFR02.fasc" will also be present here.
d) Post Processing Output: You will have to sort the score file basec
on the Interface Score (I_sc) column, such that it ranges from
smallest to largest. The ten lowest interface-scoring models are
supposed to contain at least one native-like prediction. One way of
sorting is by the following command: "sort -k7 -n aaFR02.fasc | grep
aaFR | cut -c-80 | head"


2) EnsembleDock_plus_SnugDock protocol:Directory "EnsembleDock_plus_SnugDock"
All the inputs are contained in the subdirectory
"EnsembleDock_plus_SnugDock/input/prepack_input". It contains the
following files:
1vfb.pdb: The native pdb if available
FR02.fab: The FAb constraints file similar to that when using
RosettaDock with antibody. This helps in biasing the simulation
towards interfaces containing the CDRs.
FR02.pdb: The input structure
FR02.unbound.pdb: The structure from which side-chain rotameric states
are appended to the standard Dunbrak rotamers. If an unbound is not
provided, the rotamers of the input structure are lost.
AB_model1..10.pdb: The ten antibody homology models. This can be an
ensemble of NMR structures or any ensemble as long as the sequence is
the same for all the conformers. This can be even more than ten.
pdblist1: A list of all the antibody structures to be used for
docking. (In this example, there are only ten entries corresponding to
the ten structures)
Antigen.pdb: The antigen structure to be used in docking. If an
ensemble is not present for the antigen, this is generally the antigen
contained in FR02.pdb
pdblist2: A list of the antigen structures to be used. (In this
example, there is only one entry corresponding to the one antigen)

Prepack:
a) Preparing the input: Prior to running the prepack, the subdirectory
"EnsembleDock_plus_SnugDock/input" is supposed to be empty, (It is
full because in the example prepack has already run) and one has to
copy over the contents of the "EnsembleDock_plus_SnugDock/input/prepack_input" to "EnsembleDock_plus_SnugDock/input".
b) Lauching prepack: Enter the directory
"EnsembleDock_plus_SnugDock/prepack" and execute the following command
"./prepack.bash | tee prepack.logfile" ( The portion after the pipe is
optional, and is needed if you want to store the logfile of the prepack run )


EnsembleDock_plus_SnugDock (only) run:
a) Preparing the input: In the directory
"EnsembleDock_plus_SnugDock/EnsembleDock_plus_SnugDock", change the
"EnsembleDock_plus_SnugDock.bash" file such that nstruct is 1000
(currently it is 10). Depending on the type of search (global/local), standard
RosettaDock command line flags can be used.
b) Lauching EnsembleDock_plus_SnugDock: Execute the following command
"./EnsembleDock_plus_SnugDock.bash | tee
EnsembleDock_plus_SnugDock.logfile". The portion after the pipe is
optional, and is needed if you want to store the logfile of the EnsembleDock_plus_SnugDock run. )
c) Outputs: Depending on the nstruct value, you will have a
corresponding number of output structures in the directory
"EnsembleDock_plus_SnugDock/EnsembleDock_plus_SnugDock" named
aaFR02_0001.pdb .... aaFR02_1000.pdb. ( in this example there will be
only 10 structures) A fullatom score file, "aaFR02.fasc" will also be
present here.
d) Post Processing Output: You will have to sort the score file basec
on the Interface Score (I_sc) column, such that it ranges from
smallest to largest. The ten lowest interface-scoring models are
supposed to contain at least one native-like prediction. One way of
sorting is by the following command: "sort -k10 -n aaFR02.fasc | grep
aaFR | cut -c-80 | head"