3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.
3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.
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DOI：
10.1002/prot.24167
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发表时间：
2013-01
影响因子：
2.9
通讯作者：
Cheng, Jianlin
中科院分区：
文献类型：
--
作者：
Bhattacharya, Debswapna;Cheng, Jianlin
关键词：
计算蛋白质结构预测的主要局限性之一是预测模型与实验推导的真实天然结构的偏差。这些限制往往阻碍了计算蛋白质结构预测方法在对结构细节非常敏感的生化分配和药物设计中应用的可能性。然而，将这些低分辨率预测模型改进为接近原始状态的高分辨率结构，已被证明是极具挑战性的。因此，蛋白质结构的细化在很大程度上仍然是一个未解决的问题。对蛋白质结构预测（CASP）技术的关键评估明确表明，大多数参与改进类别的预测器仍然没有始终如一地提高模型质量。在这里，我们提出了一个两步细化协议，称为3Drefine，以始终使初始模型更接近本地结构。第一步是基于氢键（HB）网络的优化，第二步是利用复合物理和基于知识的力场对优化模型进行原子级能量最小化。该方法已在CASP基准数据上进行了评估，并且在全球和局部结构质量度量中都比初始结构表现出一致的改进。3Drefine方法在计算上也很便宜，只需要几分钟的CPU时间来提炼一个典型长度的蛋白质（300个残基）。
One of the major limitations of computational protein structure prediction is the deviation of predicted models from their experimentally derived true, native structures. The limitations often hinder the possibility of applying computational protein structure prediction methods in biochemical assignment and drug design that are very sensitive to structural details. Refinement of these low-resolution predicted models to high-resolution structures close to the native state, however, has proven to be extremely challenging. Thus, protein structure refinement remains a largely unsolved problem. Critical assessment of techniques for protein structure prediction (CASP) specifically indicated that most predictors participating in the refinement category still did not consistently improve model quality. Here, we propose a two-step refinement protocol, called 3Drefine, to consistently bring the initial model closer to the native structure. The first step is based on optimization of hydrogen bonding (HB) network and the second step applies atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields. The approach has been evaluated on the CASP benchmark data and it exhibits consistent improvement over the initial structure in both global and local structural quality measures. 3Drefine method is also computationally inexpensive, consuming only few minutes of CPU time to refine a protein of typical length (300 residues).
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影响因子：
2.9
作者：
Krivov, Georgii G.;Shapovalov, Maxim V.;Dunbrack, Roland L., Jr.
通讯作者：
Dunbrack, Roland L., Jr.
影响因子：
5.8
作者：
Arakaki, AK;Zhang, Y;Skolnick, J
通讯作者：
Skolnick, J
DOI：
10.1002/prot.340040208
发表时间：
1988-01-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
BRUNGER, AT;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
2.9
作者：
Joo, Keehyoung;Lee, Jinwoo;Lee, Jooyoung
通讯作者：
Lee, Jooyoung
DOI：
10.1073/pnas.0601210103
发表时间：
2006-05-30
影响因子：
11.1
作者：
Friedel, Miriam;Baumketner, Andrij;Shea, Joan-Emma
通讯作者：
Shea, Joan-Emma