.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH PRODIGY "1" "April 2023" "prodigy 2.1.3" "User Commands"
.SH NAME
prodigy \- binding affinity predictor
.SH DESCRIPTION
usage: prodigy [\-h] [\-\-distance\-cutoff DISTANCE_CUTOFF]
.IP
[\-\-acc\-threshold ACC_THRESHOLD] [\-\-temperature TEMPERATURE]
[\-\-contact_list] [\-\-pymol_selection] [\-q] [\-V]
[\-\-selection A B [A,B C ...]]
structf
.PP
Binding affinity predictor based on Intermolecular Contacts (ICs).
.PP
Anna Vangone and Alexandre M.J.J. Bonvin,
Contacts\-based prediction of binding affinity in protein\-protein complexes.
eLife (2015)
.SS "positional arguments:"
.TP
structf
Structure to analyse in PDB or mmCIF format
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-distance\-cutoff\fR DISTANCE_CUTOFF
Distance cutoff to calculate ICs
.TP
\fB\-\-acc\-threshold\fR ACC_THRESHOLD
Accessibility threshold for BSA analysis
.TP
\fB\-\-temperature\fR TEMPERATURE
Temperature (C) for Kd prediction
.TP
\fB\-\-contact_list\fR
Output a list of contacts
.TP
\fB\-\-pymol_selection\fR
Output a script to highlight the interface (pymol)
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Outputs only the predicted affinity value
.TP
\fB\-V\fR, \fB\-\-version\fR
Print the version and exit.
.PP
Selection Options:
.IP
By default, all intermolecular contacts are taken into consideration,
a molecule being defined as an isolated group of amino acids sharing
a common chain identifier. In specific cases, for example
antibody\-antigen complexes, some chains should be considered as a
single molecule.
.IP
Use the \fB\-\-selection\fR option to provide collections of chains that should
be considered for the calculation. Separate by a space the chains that
are to be considered _different_ molecules. Use commas to include multiple
chains as part of a single group:
.HP
\fB\-\-selection\fR A B => Contacts calculated (only) between chains A and B.
.TP
\fB\-\-selection\fR A,B C => Contacts calculated (only) between
chains A and C; and B and C.
.TP
\fB\-\-selection\fR A B C => Contacts calculated (only) between
chains A and B; B and C; and A and C.
.HP
\fB\-\-selection\fR A B [A,B C ...]