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Improved low-resolution crystallographic refinement with Phenix and Rosetta.利用 Phenix 和 Rosetta 进行改进的低分辨率晶体学精修。
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2
Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.利用 PHENIX 中的 AFITT 在晶体学精修中改进配体几何形状。
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RNA Structure Refinement Using the ERRASER-Phenix Pipeline.使用ERRASER-Phenix流程进行RNA结构优化
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Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.在phenix.refine中使用基于知识的约束来改善低分辨率下的大分子精修。
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):381-90. doi: 10.1107/S0907444911047834. Epub 2012 Mar 16.
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phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.菲尼克斯（Phenix）的Rosetta分子置换与模型重建
J Struct Funct Genomics. 2012 Jun;13(2):81-90. doi: 10.1007/s10969-012-9129-3. Epub 2012 Mar 15.
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Towards automated crystallographic structure refinement with phenix.refine.利用phenix.refine实现自动化晶体学结构精修
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi: 10.1107/S0907444912001308. Epub 2012 Mar 16.
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Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.精确的大分子晶体学精修：将线性缩放半经验量子力学程序DivCon纳入PHENIX精修软件包。
Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1233-47. doi: 10.1107/S1399004714002260. Epub 2014 Apr 26.
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Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.通过将 Amber 力场集成到 Phenix 中，改进了用于晶体学精修的化学约束。
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Automated structure solution with the PHENIX suite.使用PHENIX套件进行自动化结构解析。
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Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.使用 Phenix/OPLS3e 对 X 射线和冷冻电镜结构进行大分子精修，以提高结构和配体质量。
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Conformational plasticity of a BiP-GRP94 chaperone complex.BiP-GRP94伴侣蛋白复合物的构象可塑性
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Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks.通过溶剂介导的变构网络进行高信号活性膜受体的计算设计
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Accurate de novo design of heterochiral protein-protein interactions.异手性蛋白质-蛋白质相互作用的精确从头设计。
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AQuaRef: Machine learning accelerated quantum refinement of protein structures.水参考：机器学习加速蛋白质结构的量子精修
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Structural basis of closed groove scrambling by a TMEM16 protein.TMEM16 蛋白封闭沟槽扰乱的结构基础。
Nat Struct Mol Biol. 2024 Oct;31(10):1468-1481. doi: 10.1038/s41594-024-01284-9. Epub 2024 Apr 29.
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Identification and structural analysis of a thermophilic β-1,3-glucanase from compost.来自堆肥的嗜热β-1,3-葡聚糖酶的鉴定与结构分析
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Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE.基于结构的 [4Fe-4S]-依赖型硫插入酶 LarE 机制的研究进展
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Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics.利用组合细化策略和分子动力学阐明 p53 构象体的结构变异性。
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Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger.黑曲霉中酸性脯氨酸特异性内肽酶对蛋白质水解的结构和时间分辨的机制研究。
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Delineating Conformational Variability in Small Protein Structures Using Combinatorial Refinement Strategies.使用组合优化策略描绘小蛋白质结构中的构象变异性
Micromachines (Basel). 2023 Sep 29;14(10):1869. doi: 10.3390/mi14101869.
本文引用的文献
1
Scientific benchmarks for guiding macromolecular energy function improvement.指导大分子能量函数改进的科学基准。
Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0.
2
Structure and stoichiometry of an accessory subunit TRIP8b interaction with hyperpolarization-activated cyclic nucleotide-gated channels.三聚体 G 蛋白偶联受体相互作用蛋白 8b 亚基与超极化激活环核苷酸门控通道相互作用的结构和化学计量。
Proc Natl Acad Sci U S A. 2012 May 15;109(20):7899-904. doi: 10.1073/pnas.1201997109. Epub 2012 May 1.
3
Low-resolution refinement tools in REFMAC5.REFMAC5中的低分辨率精修工具。
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):404-17. doi: 10.1107/S090744491105606X. Epub 2012 Mar 16.
4
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.将密度修改与自动模型构建应用于分子置换相位确定的一个困难案例：谷氨酸棒杆菌假定琥珀酰二氨基庚二酸去琥珀酰化酶的结构
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):391-403. doi: 10.1107/S090744491104978X. Epub 2012 Mar 16.
5
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.在phenix.refine中使用基于知识的约束来改善低分辨率下的大分子精修。
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):381-90. doi: 10.1107/S0907444911047834. Epub 2012 Mar 16.
6
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.在精修中利用结构相似性：BUSTER中的自动非晶体学对称性及目标结构约束
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):368-80. doi: 10.1107/S0907444911056058. Epub 2012 Mar 16.
7
Towards automated crystallographic structure refinement with phenix.refine.利用phenix.refine实现自动化晶体学结构精修
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi: 10.1107/S0907444912001308. Epub 2012 Mar 16.
8
Polarizable atomic multipole X-ray refinement: weighting schemes for macromolecular diffraction.可极化原子多极X射线精修：大分子衍射的加权方案
Acta Crystallogr D Biol Crystallogr. 2011 Nov;67(Pt 11):957-65. doi: 10.1107/S0907444911039060. Epub 2011 Oct 19.
9
Automated real-space refinement of protein structures using a realistic backbone move set.利用真实的骨架移动集自动进行蛋白质结构的实空间精修。
Biophys J. 2011 Aug 17;101(4):899-909. doi: 10.1016/j.bpj.2011.06.063.
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Modeling symmetric macromolecular structures in Rosetta3.在 Rosetta3 中对对称大分子结构建模。
PLoS One. 2011;6(6):e20450. doi: 10.1371/journal.pone.0020450. Epub 2011 Jun 22.
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