DOI: 10.5281/zenodo.12804207
title: FTDMP docking results for protein-protein, protein-DNA, protein-RNA benchmarks

description: FTDMP docking results for protein-protein, protein-DNA, protein-RNA benchmarks. 

FTDMP is a software system for running docking experiments and scoring/ranking multimeric models. This dataset contains FTDMP docking results for protein-protein, protein-DNA, protein-RNA benchmarks. The FTDMP framework itself is available at https://github.com/kliment-olechnovic/ftdmp. 

Every *.tar.gz file in this dataset contains two folders: results for unbound-unbound and bound-bound docking. These folders contain results for the benchmark cases:

252 folders with results for the protein-protein docking benchmark cases [1].47 folders with results for the protein-DNA docking benchmark cases [2].42 folders with results for the protein-RNA docking benchmark cases [3-6]. 

Every folder is named according to the PDB ID of the complex. The folders contain:

1. A subfolder named relaxed_top_complexes. This subfolder contains 200 pdb files of relaxed [7] top docking models.2. A text file named scoring_results-ranks.txt. It contains the names of the models (that are in the relaxed_top_complexes folder) in the ranked order. This means that the first model in the file is considered to be the best prediction by the FTDMP framework.3. A text file named cad_scores.txt. It contains interface CAD-score and binding site CAD-score [8] results for every model.4. A text file named rmsd_results.txt, which is available only for protein-DNA and protein-RNA cases. The file contains ligand-RMSD values for the models, where the DNA/RNA is considered as the ligand.5. A text file named DockQ_results.txt, which is available only for the protein-protein docking cases. The file contains DockQ [9] results for every model, as well as model accuracy based on CAPRI criteria (Incorrect, Acceptable, Medium, High)6. A text file named binding_site_CAD-scores.txt, which contains the binding site CAD-score from the protein side for RNA and DNA docking. This binding site CAD-score shows how accurately the ligand (DNA/RNA) was docked to the protein without taking the orientation of the ligand into consideration. In the case of protein-protein docking the binding site CAD-score file is available only for antibody-antigen docking targets and contains the binding site (epitope) CAD-score for the antigen.  

The ligand-RMSD, CAD-scores, and DockQ scores were all calculated by comparing the models to the corresponding targets. The target structures are available at https://zenodo.org/records/10517524. These target structures have the same residue numbering as the models available here. 

REFERENCES 

[1] Guest, J. D., et al. (2021). An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure, 29(6), 606–621.e5.[2] van Dijk, M., Bonvin, A.M. (2008). A protein-DNA docking benchmark. Nucleic Acids Res, 36, e88. [3] Perez-Cano, L., et. Al. (2012). A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data. Proteins, 80(7): 1872-1882. [4] Huang, S.Y., Zou, X. (2013). A nonredundant structure dataset for benchmarking protein-RNA computational docking. J Comput Chem, 34(4): 311-318. [5] Nithin, C., et. al. (2017). A non-redundant protein-RNA docking benchmark version 2.0. Proteins, 85(2) :256-267. [6] Zheng, J., et al. (2020). P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking. Bioinformatics, 36(1), 96–103. [7] Eastman, P., et al.(2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLOS Comp. Biol., 13(7): e1005659.  [8] Olechnovic, K., Venclovas, C. (2020). Contact area-based structural analysis of proteins and their complexes using CAD-score. Methods Mol Biol, 2112, 75.[9] Basu, S., Wallner, B. (2016). DockQ: A Quality Measure for Protein-Protein Docking Models. PLoS ONE 11(8): e0161879.