The integrative docking protocol includes a number of tools:

saxs_score

Scoring with SAXS profile.

Usage: <pdb1> <pdb2> <trans_file> <exp_profile_file>
saxs_score program scores results of docking of two molecules against the SAXS profile file.

<pdb1> - The first molecule that was given to docking program and was kept in place during docking
<pdb2> - The second molecule that was given to docking program and was transformed
<trans_file> - Docking output file with transformations that bring the transformed molecule to the static molecule.
  The format is as follows:

    1 -0.75020 0.67870 0.34160 82.62000 59.28000 -1.01100
    2 -0.42560 0.55540 0.33110 75.69000 67.15000 -0.30480
    3 -0.48910 0.66950 0.11820 84.94000 58.97000 3.34300

  The first number is the transformation number followed by three rotational and three translational parameters.

<exp_profile_file> - The SAXS profile of the complex. see https://modbase.compbio.ucsf.edu/foxs/help for format details.

em2d_score

Scoring with EM 2D class averages.

Usage: <pdb1> <pdb2> <trans_file> <image1> <image2>...
em2d_score program scores results of docking of two molecules against 2D class averages from EM.

<pdb1> <pdb2> <trans_file> as above
<image1> <image2>... - complex 2D class averages in PGM format (P2)

em3d_score

Scoring with EM 3D density map.

Usage: <pdb1> <pdb2> <trans_file> <em_map>
em3d_score program scores results of docking of two molecules against 3D density map.

<pdb1> <pdb2> <trans_file> as above
<em_map> - density map of the complex in mrc format

nmr_rtc_score

Scoring with NMR residue type content term (NMR-RTC).

Usage: <pdb1> <pdb2> <trans_file> <residue_content_file1> <residue_content_file2>
nmr_rtc_score program scores results of docking of two molecules against NMR residue type content.
NMR residue type content data provides us with information about residue composition at the interface.
For example, we can know that the interface has 2 arginine and 3 histidine residues.

<pdb1> <pdb2> <trans_file> as above
<residue_content_file1> - residue content file for pdb1 or '-' if none
<residue_content_file2> - residue content file for pdb2 or '-' if none
  The format of the file is as follows:

MET 0
ARG 0
HIS 2

  This would correspond to having 0 methionine, 0 arginine and two histidine residues in the interface.

cross_links_score

Scoring with cross links detected by mass spectrometry.

Usage: <pdb1> <pdb2> <trans_file> <cross_links_file>
cross_links_score program scores results of docking of two molecules against cross linking dataset.

<pdb1> <pdb2> <trans_file> as above
<cross_links_file> - file with detected cross links

  The format of the file is as follows:
145 - 1 A 3 27
224 - 1 A 3 27
169 - 1 A 3 27
222 - 1 A 3 27

Each line corresponds to one cross link. Each cross link is defined by residue numbers and chain ids of the cross linked residues, followed by limits on the distance between CA atoms.

'145 - 1 A 3 27' corresponds to a cross link between residue 145 in a chain with blank chain id and residue 1 in chain A. The minimal distance is 3A and the maximal is 27A.

combine_scores

Combine scores for different data types.

Usage: combine_scores <file1> <weight1> <file2> <weight2> <file3> <weight3>...
combines files with same docking transformations in the following format:

# | score | filtered (+/-) | z-score | ... | Transformation

The programs for scoring of docking transformations (saxs_score, em2d_score, em3d_score, nmr_rtc_score) output results in this format.

Only filtered values of + are combined. The output score is the weighted sum of Z-Scores.

recompute_zscore

Recompute z-scores for combined scores.

em3d_single_score

Score a single model with EM3D.

em2d_single_score

Score a single model with EM2D.

soap_score

Score models with SOAP.

cross_links_single_score

Score a single model with cross links.

interface_cross_links

Generate cross links for an interface.

interface_rtc

Generate residue content for an interface.