CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.
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DOI：
10.1021/acs.jcim.5b00387
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发表时间：
2016-06-27
影响因子：
5.6
通讯作者：
Carlson HA
中科院分区：
文献类型：
--
作者：
Smith RD;Damm-Ganamet KL;Dunbar JB Jr;Ahmed A;Chinnaswamy K;Delproposto JE;Kubish GM;Tinberg CE;Khare SD;Dou J;Doyle L;Stuckey JA;Baker D;Carlson HA
社区结构活动资源（CSAR）进行了一项基准测试，以评估当前用于蛋白质设计、配体对接和评分/排名的计算方法。这项工作分三个阶段进行。第一阶段要求参与者识别并排列能够结合小分子地高辛的设计序列。第二阶段的挑战社区选择一个接近天然的姿态地高辛从一组诱饵构成的两个设计的蛋白质。第三阶段研究了当前方法对10种相关类固醇与所设计的蛋白质之一的结合亲和力进行排名/评分的能力。我们发现，13组中有11组能够正确选择结合地高辛的序列，大多数组为蛋白质的骨架以及活性位点残基的所有原子提供正确的三维结构。14组中有11组能够从一组看似合理的诱饵姿势中选择合适的姿势。预测绝对结合亲和力的能力仍然是一项困难的任务，因为14组中的8组能够将分数与设计的蛋白质对同源类固醇的亲和力（Pearson-r > 0.7）相关联，并且14组中仅5组能够将10种相关配体的等级相关联（斯皮尔曼-ρ > 0.7）。
The Community Structure Activity Resource (CSAR) conducted a benchmark exercise to evaluate the current computational methods for protein design, ligand docking, and scoring/ranking. The exercise consisted of three phases. The first phase required the participants to identify and rank order which designed sequences were able to bind the small molecule digoxigenin. The second phase challenged the community to select a near-native pose of digoxigenin from a set of decoy poses for two of the designed proteins. The third phase investigated the ability of current methods to rank/score the binding affinity of 10 related steroids to one of the designed proteins. We found that eleven of thirteen groups were able to correctly select the sequence that bound digoxigenin, with most groups providing the correct three-dimensional structure for the backbone of the protein as well as all atoms of the active-site residues. Eleven of the fourteen groups were able to select the appropriate pose from a set of plausible decoy poses. The ability to predict absolute binding affinities is still a difficult task, as 8 of 14 groups were able to correlate scores to affinity (Pearson-r > 0.7) of the designed protein for congeneric steroids and only 5 of 14 groups were able to correlate the ranks of the 10 related ligands (Spearman-ρ > 0.7).
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影响因子：
5.6
作者：
Hu B;Zhu X;Monroe L;Bures MG;Kihara D
通讯作者：
Kihara D
影响因子：
5.6
作者：
Dunbar JB Jr;Smith RD;Yang CY;Ung PM;Lexa KW;Khazanov NA;Stuckey JA;Wang S;Carlson HA
通讯作者：
Carlson HA
影响因子：
5.6
作者：
Damm-Ganamet KL;Smith RD;Dunbar JB Jr;Stuckey JA;Carlson HA
通讯作者：
Carlson HA
影响因子：
5.6
作者：
Dunbar JB Jr;Smith RD;Damm-Ganamet KL;Ahmed A;Esposito EX;Delproposto J;Chinnaswamy K;Kang YN;Kubish G;Gestwicki JE;Stuckey JA;Carlson HA
通讯作者：
Carlson HA
影响因子：
2.9
作者：
Jacobson, MP;Pincus, DL;Friesner, RA
通讯作者：
Friesner, RA