RF models and selected data from the protein-peptide RF scoring paper
The PDBQT files in the receptors and peptides folders are the files provided by the authors of:
Robert Rentzsch, Bernhard Y. Renard, Docking small peptides remains a great challenge: an assessment using AutoDock Vina, Briefings in Bioinformatics, Volume 16, Issue 6, November 2015, Pages 1045–1056, https://doi.org/10.1093/bib/bbv008
This excel spreadsheet provides the 21 random splits performed on the training subset to create 12 validation and learnign sets.
use tar zxvf classifiers.tgz to expand this file into the classifier folder containing the pickled RF models described in the paper:
Michel F. Sanner, Leonard Dieguez, Stefano Forli, Ewa Lis. Improving Docking Power for peptides using Random Forest, JCIM ...
This comma separated file provides for each entry the complex name, the list of protein chains ID(s) and the number and length of these chains, the chain ID(s) short peptidic chains (i.e. chains with less than 50 amino acids and different from the peptide ligand) their number and length