One contact for every twelve residues allows robust and accurate topology-level protein structure modeling.
One contact for every twelve residues allows robust and accurate topology-level protein structure modeling.
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DOI：
10.1002/prot.24374
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发表时间：
2014-02
影响因子：
2.9
通讯作者：
Baker, David
中科院分区：
文献类型：
--
作者：
Kim, David E.;DiMaio, Frank;Wang, Ray Yu-Ruei;Song, Yifan;Baker, David
已经描述了多种方法来识别蛋白质三维结构中的接触残基对，但尚不清楚精确的结构建模需要多少接触残基。 CASP10 辅助接触实验提供了接触引导蛋白质结构建模的盲测。我们使用 Rosetta 结构建模方法描述了针对这些接触引导预测挑战生成的模型。对于几乎所有情况，提交的模型都具有正确的整体拓扑，并且在某些情况下，它们具有接近原子级的精度；例如，384 个残基同源寡聚四聚体 (Tc680o) 的模型与晶体结构的均方根偏差 (RMSD) 仅 2.9 Å。我们的结果表明，用于获取接触信息的实验和生物信息学方法可能只需要为蛋白质中的每 12 个残基生成一个正确的接触，即可实现准确的拓扑水平建模。
A number of methods have been described for identifying pairs of contacting residues in protein three-dimensional structures, but it is unclear how many contacts are required for accurate structure modeling. The CASP10 assisted contact experiment provided a blind test of contact guided protein structure modeling. We describe the models generated for these contact guided prediction challenges using the Rosetta structure modeling methodology. For nearly all cases, the submitted models had the correct overall topology, and in some cases, they had near atomic-level accuracy; for example the model of the 384 residue homo-oligomeric tetramer (Tc680o) had only 2.9 Å root-mean-square deviation (RMSD) from the crystal structure. Our results suggest that experimental and bioinformatic methods for obtaining contact information may need to generate only one correct contact for every 12 residues in the protein to allow accurate topology level modeling.
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影响因子：
5.6
作者：
Schmitz, Christophe;Vernon, Robert;Otting, Gottfried;Baker, David;Huber, Thomas
通讯作者：
Huber, Thomas
影响因子：
2.9
作者：
Chan, Kwok-Yan;Trabuco, Leonardo G.;Schreiner, Eduard;Schulten, Klaus
通讯作者：
Schulten, Klaus
影响因子：
2.9
作者：
Das, Rhiju;Bin Qian;Baker, David
通讯作者：
Baker, David
DOI：
10.1073/pnas.0610313104
发表时间：
2007-06-05
影响因子：
11.1
作者：
Cavalli, Andrea;Salvatella, Xavier;Vendruscolo, Michele
通讯作者：
Vendruscolo, Michele
DOI：
10.1002/prot.10499
发表时间：
2003-11-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
Li, W;Zhang, Y;Skolnick, J
通讯作者：
Skolnick, J