High accuracy template based modeling by global optimization
High accuracy template based modeling by global optimization
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DOI：
10.1002/prot.21628
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发表时间：
2007-01-01
影响因子：
2.9
通讯作者：
Lee, Jooyoung
中科院分区：
文献类型：
--
作者：
Joo, Keehyoung;Lee, Jinwoo;Lee, Jooyoung
对于基于模板的CASP7靶的高精度建模，我们应用了一种基于分数函数的严格优化的过程，分三个阶段：多重比对、链构建和侧链建模。我们将构象空间退火法应用于一种新的基于一致性的多重比对得分函数。对于链式构筑，我们对模型能量函数进行了优化。对于侧链建模，我们使用针对给定靶序列构建的旋转异构体文库优化了类似SCWRL的能量函数。通过严格的优化，我们在TBM和TBM/HA目标的主链和侧链建模方面取得了显著的改进。对于大多数TBM/HA靶点(17/26)，预测模型比以后验方式从最佳模板构建的模型更准确。目前的方法似乎可以从多个模板中提取相关信息。
For high-accuracy template-based-modeling of CASP7 targets, we have applied a procedure based on the rigorous optimization Of score functions at three stages: multiple alignment, chain building, and side-chain modeling. We applied the conformational space annealing method to a newly developed consistency based score function for multiple alignment. For chain building, we optimized the MODELLER energy function. For side-chain modeling, we optimized a SCWRL-like energy function using a rotamer library constructed specifically for a given target sequence. By rigorous optimization, we have achieved significant improvement in backbone as well as side-chain modeling for TBM and TBM/HA targets. For most TBM/HA targets (17/26), the predicted model was more accurate than the model one can construct from the best template in a posteriori fashion. It appears that the current method can extract relevant information out of multiple templates.