A protein-protein docking decoys set from three different rigid body methods
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This set of decoys was generated for the targets in the Protein-Protein Docking Benchmark 5 (Vreven <em>et al.</em>, 2015), using ZDock (Chen <em>et al.</em>, 2003), FTDock (Gabb <em>et al.</em>, 1997), and HADDOCK (only the FFT phase) (Dominguez <em>et al.</em>, 2003; de Vries <em>et al.</em>, 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 <em>et al.</em>, 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.: <br> <strong>H</strong>_<strong>CP57</strong>_<strong>2211</strong>_<strong>I</strong>.pdb H <- Haddock CP57 <- BM5 id label 2211 <- decoy number I <- CAPRI quality (H)high, (M)medium , (A)acceptable ,(I)Incorrect References: Chen,R. <em>et al.</em> (2003) ZDOCK: an initial-stage protein-docking algorithm. <em>Proteins</em>, <strong>52</strong>, 80–87. Dominguez,C. <em>et al.</em> (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. <em>J Am Chem Soc</em>, <strong>125</strong>, 1731–1737. Gabb,H.A. <em>et al.</em> (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. <em>J Mol Biol</em>, <strong>272</strong>, 106–120. Lensink,M.F. <em>et al.</em> (2007) Docking and scoring protein complexes: CAPRI 3rd Edition. <em>Proteins</em>, <strong>69</strong>, 704–718. Vreven,T. <em>et al.</em> (2015) Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. <em>Journal of Molecular Biology</em>, <strong>427</strong>, 3031–3041. de Vries,S.J. <em>et al.</em> (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. <em>Proteins</em>, <strong>69</strong>, 726–733.
