Scoring optimisation of unbound protein–protein docking including protein binding site predictions
Scoring optimisation of unbound protein–protein docking including protein binding site predictions
复制标题
未结合蛋白质-蛋白质对接的评分优化，包括蛋白质结合位点预测
DOI：
10.1002/jmr.1165
复制
发表时间：
2012
影响因子：
2.7
通讯作者：
Zacharias M
中科院分区：
文献类型：
--
作者：
Schneider S;Zacharias M
蛋白质-蛋白质复合体结构的预测对于更好地理解分子识别过程具有重要意义。在系统的蛋白质-蛋白质对接过程中，蛋白质分子的表面被扫描以寻找假定的配对蛋白质的结合位置。系统地探索了在对接过程中基于实验或生物信息学预测的假定结合位点包括外部数据的可能性。外部数据在与粗粒蛋白质模型对接期间被包括在内，并基于力场权重来将对接搜索偏向预测或已知的结合区域。该方法在一大组非结合构象的蛋白质伙伴上进行了测试。如果有关于天然结合位点的可靠数据，则发现对接性能显著改善。即使包括结合界面上单一关键氨基酸的数据，这也是可能的。在结合位点预测精度有限的情况下，与无偏向对接相比，仅发现略有改善。研究发现，将搜索偏向于预测的结合位点的协议的优化进一步提高了对接性能，导致在前10个对接预测中产生了大约40%的可接受解决方案，而在未结合蛋白质结构的无偏见对接的情况下，这一比例为22%。版权所有©2011 John Wiley&Sons，Ltd.
The prediction of the structure of the protein–protein complex is of great importance to better understand molecular recognition processes. During systematic protein–protein docking, the surface of a protein molecule is scanned for putative binding sites of a partner protein. The possibility to include external data based on either experiments or bioinformatic predictions on putative binding sites during docking has been systematically explored. The external data were included during docking with a coarse‐grained protein model and on the basis of force field weights to bias the docking search towards a predicted or known binding region. The approach was tested on a large set of protein partners in unbound conformations. The significant improvement of the docking performance was found if reliable data on the native binding sites were available. This was possible even if data for single key amino acids at a binding interface are included. In case of binding site predictions with limited accuracy, only modest improvement compared with unbiased docking was found. The optimisation of the protocol to bias the search towards predicted binding sites was found to further improve the docking performance resulting in approximately 40% acceptable solutions within the top 10 docking predictions compared with 22% in case of unbiased docking of unbound protein structures. Copyright © 2011 John Wiley & Sons, Ltd.
影响因子：
2.9
作者：
de Vries, Sjoerd J.;Melquiond, Adrien S. J.;Bonvin, Alexandre M. J. J.
通讯作者：
Bonvin, Alexandre M. J. J.
一种使用预测的蛋白质-蛋白质结合位点对对接蛋白质复合物进行评分的新方法。
DOI：
--
发表时间：
2004
期刊：
Protein engineering, design & selection : PEDS
影响因子：
--
作者：
K. Gottschalk;Hani Neuvirth;G. Schreiber
通讯作者：
G. Schreiber