A protein-protein docking decoys set from three different rigid body methods

Abstract
This set of decoys was generated for the targets in the Protein-Protein Docking Benchmark 5 (Vreven et al., 2015), using ZDock (Chen et al., 2003), FTDock (Gabb et al., 1997), and HADDOCK (only the FFT phase) (Dominguez et al., 2003; de Vries et al., 2007). Included are only those targets for which at least one correct decoy could be generated. Decoys were analyzed with the CAPRI quality standards (Lensink et al., 2007), based on the comparison to the corresponding target experimental structure. For each decoy, all the needed information is reported in its name, e.g.: H_CP57_2211_I.pdb H <- Haddock CP57 <- BM5 id label 2211 <- decoy number I <- CAPRI quality (H)high, (M)medium , (A)acceptable ,(I)Incorrect References: Chen,R. et al. (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins, 52, 80–87. Dominguez,C. et al. (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc, 125, 1731–1737. Gabb,H.A. et al. (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol, 272, 106–120. Lensink,M.F. et al. (2007) Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins, 69, 704–718. Vreven,T. et al. (2015) Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology, 427, 3031–3041. de Vries,S.J. et al. (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins, 69, 726–733.

Citation
Barradas-Bautista, D., Oliva, R., & Cavallo, L. (2020). A protein-protein docking decoys set from three different rigid body methods (one) [Data set]. Zenodo. https://doi.org/10.5281/ZENODO.4012018

Publisher
Zenodo

DOI
10.5281/zenodo.4012018

Additional Links
https://zenodo.org/record/4012018

Relations
Is Supplement To:
  • [Article]
    Barradas-Bautista, D., Cao, Z., Vangone, A., Oliva, R., & Cavallo, L. (2021). A Random Forest Classifier for Protein-Protein Docking Models. Bioinformatics Advances. doi:10.1093/bioadv/vbab042. DOI: 10.1093/bioadv/vbab042 Handle: 10754/669803
  • [Preprint]
    Barradas-Bautista, D., Cao, Z., Vangone, A., Oliva, R., & Cavallo, L. (2021). A Random Forest Classifier for Protein-Protein Docking Models. doi:10.1101/2021.06.23.449420. DOI: 10.1101/2021.06.23.449420 Handle: 10754/669803

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