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.
本数据集的诱饵构象均针对蛋白质-蛋白质对接基准数据集5（Protein-Protein Docking Benchmark 5，Vreven等，2015）中的靶标生成，所用工具包括ZDock（Chen等，2003）、FTDock（Gabb等，1997）以及仅采用快速傅里叶变换（FFT）阶段的HADDOCK（Dominguez等，2003；de Vries等，2007）。 本数据集仅收录至少可生成一个正确诱饵构象的靶标。 所有诱饵构象均依据交互预测关键评估（CAPRI）质量标准（Lensink等，2007）进行质量评价，评价基准为对应靶标的实验结构。 每个诱饵构象的全部必要信息均包含于其文件名中，示例如下：<br> <strong>H</strong>_<strong>CP57</strong>_<strong>2211</strong>_<strong>I</strong>.pdb，其中各部分含义为：H代表所用工具为HADDOCK，CP57为基准数据集5（BM5）的靶标标识，2211为诱饵编号，I为CAPRI质量等级，(H)代表高质量、(M)代表中等质量、(A)代表可接受质量、(I)代表不合格。 参考文献： Chen,R. 等（2003）ZDOCK：一种蛋白质对接初始阶段算法。《Proteins》，第52卷，80–87页。 Dominguez,C. 等（2003）HADDOCK：一种基于生化或生物物理信息的蛋白质-蛋白质对接方法。《美国化学会志》（J Am Chem Soc），第125卷，1731–1737页。 Gabb,H.A. 等（1997）基于形状互补性、静电作用与生化信息的蛋白质对接建模。《分子生物学杂志》（J Mol Biol），第272卷，106–120页。 Lensink,M.F. 等（2007）蛋白质复合物对接与打分：CAPRI第三版。《Proteins》，第69卷，704–718页。 Vreven,T. 等（2015）整合蛋白质-蛋白质相互作用基准的更新：对接基准数据集第5版与亲和力基准数据集第2版。《分子生物学杂志》（Journal of Molecular Biology），第427卷，3031–3041页。 de Vries,S.J. 等（2007）HADDOCK与HADDOCK：HADDOCK2.0在CAPRI靶标中的新特性与性能。《Proteins》，第69卷，726–733页。
