### General information

Author: Gabriele Pozzati
Contact e-mail: gabriele.pozzati@scilifelab.se
DOI: https://doi.org/10.1101/2021.08.25.457642 
License: CC0
This readme file was last updated: 01-09-2021

### Dataset description

This dataset contains docking results for the study "Improved protein docking by predicted interface residues."
In detail, it contains:
- roto-translations produced by GRAMM
- ten top ranked docking structures, generated by GRAMM and ranked according to different interface constraints
- output from the scoring script, containing information on the ranking scores
- aace18 scoring function output structures
- output of DockQ program for docking quality assessment obtained comparing dockings to native bound and unbound structures

Detailed methods adopted to generate these files are described in the DOI-linked paper.

Data and software to reproduce this dataset is available at github page: 
https://github.com/ElofssonLab/BindingSite_docking

### Available data

- files with extension ".res":
	output of GRAMM scan stage, 340000 roto-translations of the complex ligand (chain B in every structure)  

- files with extension ".pdb": 
	output structures of a complete protein-protein docking procedure (pose generation and scoring)
	using certain interface predictions as constraints (each folder involves a certain method/criteria 
	to produce constraints)
	
- files with extension ".rank":
	output of aace18 scoring function related to GRAMM output

- files terminating with "_N.pdb": 
	native structures of certain protein-protein interaction with b-factor fields substituted by 
	residue constraint values.
	
- files terminating with "_rep":
	list of scores for the top 10 ranked docking poses calculated from the scoring function described 
	in the referenced paper, as well as the same score obtained for the native structure (pose N).
	
- files terminating with "_resultsu":
	output of the DockQ program (https://github.com/bjornwallner/DockQ) for the relative 10 docking poses 
	against unbound native structure
	
- files terminating with "_resultsb":
	output of the DockQ program (https://github.com/bjornwallner/DockQ) for the relative 10 docking poses 
	against bound native structure
	
- files with "summary" prefix:
	list of DockQ program outputs for every complex docking given a specific constraints set