PRIMO/PRIMONA：一种用于蛋白质和核酸的粗粒度模型，可保持近乎原子级精度。
PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy.
机构信息
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
出版信息
Proteins. 2010 Apr;78(5):1266-81. doi: 10.1002/prot.22645.
Abstract
The new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed. This model combines one to several heavy atoms into coarse-grained sites that are chosen to allow an analytical, high-resolution reconstruction of all-atom models based on molecular bonding geometry constraints. The accuracy of proposed reconstruction method in terms of structure and energetics is tested and compared with other popular reconstruction methods for a variety of protein and nucleic acid test sets.
摘要
提出了一种新的蛋白质和核酸粗粒化模型 PRIMO/PRIMONA。该模型将一个或多个重原子组合成粗粒化位点，这些位点的选择是基于分子键几何约束，以允许对全原子模型进行分析和高分辨率重建。所提出的重建方法在结构和能量学方面的准确性进行了测试，并与其他流行的重建方法在各种蛋白质和核酸测试集上进行了比较。
相似文献
1
PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy.PRIMO/PRIMONA：一种用于蛋白质和核酸的粗粒度模型，可保持近乎原子级精度。
Proteins. 2010 Apr;78(5):1266-81. doi: 10.1002/prot.22645.
2
Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.使用各向异性 Gay-Berne 和电多极势的核酸粗粒化建模。
J Chem Theory Comput. 2016 Feb 9;12(2):676-93. doi: 10.1021/acs.jctc.5b00903. Epub 2016 Jan 15.
3
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.模拟单链结合蛋白和核酸二级结构的相互作用。
Bioinformatics. 2010 Jan 1;26(1):61-7. doi: 10.1093/bioinformatics/btp627. Epub 2009 Nov 4.
4
REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.REACH粗粒度生物分子模拟：不同蛋白质结构类别之间的可转移性
Biophys J. 2008 Aug;95(4):1639-48. doi: 10.1529/biophysj.108.131714. Epub 2008 May 9.
5
Comparison of mode analyses at different resolutions applied to nucleic acid systems.应用于核酸系统的不同分辨率下的模式分析比较。
Biophys J. 2005 Nov;89(5):2939-49. doi: 10.1529/biophysj.105.065664. Epub 2005 Aug 12.
6
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.MOLPROBITY：核酸及其复合物的结构验证与全原子接触分析
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W615-9. doi: 10.1093/nar/gkh398.
7
Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.蛋白质的 CHARMM 和 PRIMO 力场直接耦合的混合全原子/粗粒模拟。
J Chem Theory Comput. 2017 Nov 14;13(11):5753-5765. doi: 10.1021/acs.jctc.7b00840. Epub 2017 Oct 19.
8
Editorial preface.编辑前言。
Biochim Biophys Acta. 2015 May;1850(5):859-860. doi: 10.1016/j.bbagen.2015.01.010. Epub 2015 Jan 20.
9
Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics.基于导向分子动力学的碱基驱动反映射程序对核酸的作用和限制。
Biochem Biophys Res Commun. 2018 Mar 29;498(2):352-358. doi: 10.1016/j.bbrc.2017.12.057. Epub 2017 Dec 14.
10
Molecular dynamics simulations of nucleic acid-protein complexes.核酸-蛋白质复合物的分子动力学模拟
Curr Opin Struct Biol. 2008 Apr;18(2):194-9. doi: 10.1016/j.sbi.2007.12.012. Epub 2008 Feb 20.
引用本文的文献
1
A coarse-grained model for disordered and multi-domain proteins.一种针对无序和多结构域蛋白质的粗粒度模型。
Protein Sci. 2024 Nov;33(11):e5172. doi: 10.1002/pro.5172.
2
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.CHARMM 45：可访问性、功能和速度的增强。
J Phys Chem B. 2024 Oct 17;128(41):9976-10042. doi: 10.1021/acs.jpcb.4c04100. Epub 2024 Sep 20.
3
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems.GENESIS CGDYN：用于异质生物分子系统的具有动态负载平衡的大规模粗粒度 MD 模拟。
Nat Commun. 2024 Apr 20;15(1):3370. doi: 10.1038/s41467-024-47654-1.
4
Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.计算方法在拥挤细胞环境中预测蛋白质-蛋白质相互作用。
Chem Rev. 2024 Apr 10;124(7):3932-3977. doi: 10.1021/acs.chemrev.3c00550. Epub 2024 Mar 27.
5
Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.基于混合分辨率模型的超大生物分子功能运动模拟
J Chem Theory Comput. 2024 Mar 12;20(5):2228-2245. doi: 10.1021/acs.jctc.3c01046. Epub 2024 Feb 19.
6
From simple to complex: Reconstructing all-atom structures from coarse-grained models using cg2all.从简单到复杂：使用 cg2all 从粗粒模型重建全原子结构。
Structure. 2024 Jan 4;32(1):5-7. doi: 10.1016/j.str.2023.12.004.
7
One bead per residue can describe all-atom protein structures.一个珠位代表一个残基，可以描述全原子蛋白质结构。
Structure. 2024 Jan 4;32(1):97-111.e6. doi: 10.1016/j.str.2023.10.013. Epub 2023 Nov 23.
8
RNA origami: design, simulation and application.RNA 折纸：设计、模拟与应用。
RNA Biol. 2023 Jan;20(1):510-524. doi: 10.1080/15476286.2023.2237719.
9
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.在GENESIS中实现用于大规模分子动力学模拟的残基级粗粒度模型。
PLoS Comput Biol. 2022 Apr 5;18(4):e1009578. doi: 10.1371/journal.pcbi.1009578. eCollection 2022 Apr.
10
Searching for Low Probability Opening Events in a DNA Sliding Clamp.寻找DNA滑动夹中的低概率开放事件。
Life (Basel). 2022 Feb 9;12(2):261. doi: 10.3390/life12020261.
本文引用的文献
1
Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?丙氨酰二肽是代表蛋白质骨架扭转倾向的良好模型吗？
J Chem Theory Comput. 2008 Sep 9;4(9):1555-64. doi: 10.1021/ct800153n.
2
The MARTINI Coarse-Grained Force Field: Extension to Proteins.MARTINI 粗粒化力场：在蛋白质中的扩展。
J Chem Theory Comput. 2008 May;4(5):819-34. doi: 10.1021/ct700324x.
3
All-atom empirical potential for molecular modeling and dynamics studies of proteins.蛋白质分子建模和动力学研究的全原子经验势。
J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.
4
Improved prediction of protein side-chain conformations with SCWRL4.使用 SCWRL4 提高蛋白质侧链构象预测。
Proteins. 2009 Dec;77(4):778-95. doi: 10.1002/prot.22488.
5
Solvent-free lipid bilayer model using multiscale coarse-graining.使用多尺度粗粒化的无溶剂脂质双层模型
J Phys Chem B. 2009 Apr 2;113(13):4443-55. doi: 10.1021/jp810440c.
6
Reconstructing atomistic detail for coarse-grained models with resolution exchange.通过分辨率交换为粗粒度模型重建原子细节。
J Chem Phys. 2008 Sep 21;129(11):114103. doi: 10.1063/1.2976663.
7
Peptide folding using multiscale coarse-grained models.使用多尺度粗粒度模型的肽折叠
J Phys Chem B. 2008 Oct 16;112(41):13079-90. doi: 10.1021/jp8015968. Epub 2008 Sep 20.
8
Packaging double-helical DNA into viral capsids: structures, forces, and energetics.将双螺旋DNA包装进病毒衣壳：结构、作用力与能量学
Biophys J. 2008 Jul;95(2):497-502. doi: 10.1529/biophysj.108.131797. Epub 2008 May 16.
9
Insights on protein-DNA recognition by coarse grain modelling.通过粗粒度建模对蛋白质-DNA识别的见解。
J Comput Chem. 2008 Nov 30;29(15):2582-92. doi: 10.1002/jcc.21014.
10
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.基于离散分子动力学的从头算RNA折叠：从结构预测到折叠机制
RNA. 2008 Jun;14(6):1164-73. doi: 10.1261/rna.894608. Epub 2008 May 2.
Zotero 插件