Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations.
作者信息
Romo Tod D, Grossfield Alan
机构信息
Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
出版信息
Biophys J. 2014 Apr 15;106(8):1553-4. doi: 10.1016/j.bpj.2014.03.007.
Abstract
摘要
相似文献
1
Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations.未知的未知因素：分子动力学模拟中系统误差和统计误差带来的挑战。
Biophys J. 2014 Apr 15;106(8):1553-4. doi: 10.1016/j.bpj.2014.03.007.
2
Indolicidin binding induces thinning of a lipid bilayer.吲哚杀菌素结合导致脂质双分子层变薄。
Biophys J. 2014 Apr 15;106(8):L29-31. doi: 10.1016/j.bpj.2014.02.031.
3
Modulation of Antimicrobial Peptide Potency in Stressed Lipid Bilayers.应激脂质双层中抗菌肽效力的调节。
Phys Rev Lett. 2019 May 24;122(20):208103. doi: 10.1103/PhysRevLett.122.208103.
4
Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations.设计的抗菌肽MB21与截短的皮抑素S3与脂质双层的相互作用：分子动力学模拟
Biochem J. 2003 Feb 15;370(Pt 1):233-43. doi: 10.1042/BJ20021255.
5
Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.抗菌肽模拟以及力场对脂质双分子层中孔形成自由能的影响。
J Chem Theory Comput. 2016 Sep 13;12(9):4524-33. doi: 10.1021/acs.jctc.6b00265. Epub 2016 Aug 30.
6
Antimicrobial action of the cationic peptide, chrysophsin-3: a coarse-grained molecular dynamics study.阳离子肽 Chrysophsin-3 的抗菌作用：粗粒度分子动力学研究。
Soft Matter. 2018 Apr 18;14(15):2796-2807. doi: 10.1039/c7sm02152f.
7
Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers.鉴定 Pardaxin 早期插入不同磷脂双层结构中的关键残基。
J Chem Inf Model. 2017 Apr 24;57(4):929-941. doi: 10.1021/acs.jcim.6b00693. Epub 2017 Mar 27.
8
Computer simulation of antimicrobial peptides.抗菌肽的计算机模拟
Curr Med Chem. 2007;14(26):2789-98. doi: 10.2174/092986707782360105.
9
The importance of membrane defects-lessons from simulations.膜缺陷的重要性：模拟研究的启示。
Acc Chem Res. 2014 Aug 19;47(8):2244-51. doi: 10.1021/ar4002729. Epub 2014 Jun 3.
10
The discreet charm of the curve.曲线的含蓄魅力。
Biophys J. 2013 Mar 19;104(6):1215-6. doi: 10.1016/j.bpj.2013.01.046.
引用本文的文献
1
Advanced computational approaches to understand protein aggregation.用于理解蛋白质聚集的先进计算方法。
Biophys Rev (Melville). 2024 Apr 24;5(2):021302. doi: 10.1063/5.0180691. eCollection 2024 Jun.
2
Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups.计算模型预测了配备胍基羰基吡咯基团的发光配体的蛋白质结合位点。
Beilstein J Org Chem. 2022 Sep 23;18:1322-1331. doi: 10.3762/bjoc.18.137. eCollection 2022.
3
Effects of cholesterol on the mechanism of fengycin, a biofungicide.胆固醇对生物杀菌剂fengycin 作用机制的影响。
Biophys J. 2022 May 17;121(10):1963-1974. doi: 10.1016/j.bpj.2022.04.006. Epub 2022 Apr 14.
4
Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators.分子动力学：研究离子通道调节剂药物化学的强大工具。
RSC Med Chem. 2021 Jul 22;12(9):1503-1518. doi: 10.1039/d1md00140j. eCollection 2021 Sep 23.
5
In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides.基于计算机的膜活性肽结合、折叠、插入和整体稳定性预测。
Methods Mol Biol. 2021;2315:161-182. doi: 10.1007/978-1-0716-1468-6_10.
6
The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling.质膜作为 KRas4B 信号的竞争性抑制剂和正别构调节剂。
Biophys J. 2020 Mar 10;118(5):1129-1141. doi: 10.1016/j.bpj.2019.12.039. Epub 2020 Jan 22.
7
Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.基于分子模拟的 RNA 发夹结构化学精确相对折叠稳定性。
J Chem Theory Comput. 2018 Dec 11;14(12):6598-6612. doi: 10.1021/acs.jctc.8b00633. Epub 2018 Nov 27.
8
Insights from molecular dynamics simulations for computational protein design.用于计算蛋白质设计的分子动力学模拟见解。
Mol Syst Des Eng. 2017 Feb 1;2(1):9-33. doi: 10.1039/C6ME00083E. Epub 2017 Jan 9.
9
Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method.使用加权系综方法模拟窄离子通道的电流-电压关系。
J Chem Theory Comput. 2015 Apr 14;11(4):1907-18. doi: 10.1021/ct501134s.
10
Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity.胶束形成和膜融合的热力学调节抗菌脂肽活性。
Biophys J. 2015 Aug 18;109(4):750-9. doi: 10.1016/j.bpj.2015.07.011.
本文引用的文献
1
Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation.分子动力学模拟中的块协方差重叠方法与收敛性
J Chem Theory Comput. 2011 Aug 9;7(8):2464-72. doi: 10.1021/ct2002754. Epub 2011 Jul 1.
2
Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal.通过沿双层法线进行随机游走加速脂质膜中溶质分子动力学模拟的收敛
J Chem Theory Comput. 2013 Aug 13;9(8):3686-703. doi: 10.1021/ct301005b. Epub 2013 Jul 17.
3
Indolicidin binding induces thinning of a lipid bilayer.吲哚杀菌素结合导致脂质双分子层变薄。
Biophys J. 2014 Apr 15;106(8):L29-31. doi: 10.1016/j.bpj.2014.02.031.
4
Quantifying uncertainty and sampling quality in biomolecular simulations.量化生物分子模拟中的不确定性和采样质量。
Annu Rep Comput Chem. 2009 Jan 1;5:23-48. doi: 10.1016/S1574-1400(09)00502-7.
5
Convergence of molecular dynamics simulations of membrane proteins.膜蛋白分子动力学模拟的收敛性。
Proteins. 2007 Apr 1;67(1):31-40. doi: 10.1002/prot.21308.
Zotero 插件