HYDRO：一个用于预测大分子流体动力学性质的计算机程序。
HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules.
作者信息
Garcia de la Torre J, Navarro S, Lopez Martinez M C, Diaz F G, Lopez Cascales J J
机构信息
Departamento de Quimica Fisica, Universidad de Murcia, Spain.
出版信息
Biophys J. 1994 Aug;67(2):530-1. doi: 10.1016/S0006-3495(94)80512-0.
Abstract
HYDRO is a program for the calculation of sedimentation and diffusion coefficients, rotational relaxation times, and intrinsic viscosities of rigid macromolecules of arbitrary shape that are represented by bead models. Actually, HYDRO contains various FORTRAN callable subroutines that can be linked to the user's own programs to account for variability of shape or flexibility. Some hints are given for the use of HYDRO in various situations.
摘要
HYDRO是一个用于计算由珠子模型表示的任意形状刚性大分子的沉降系数、扩散系数、旋转弛豫时间和特性粘度的程序。实际上，HYDRO包含各种可通过FORTRAN调用的子程序，这些子程序可与用户自己的程序链接，以考虑形状的可变性或柔韧性。文中给出了在各种情况下使用HYDRO的一些提示。
相似文献
1
HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules.HYDRO：一个用于预测大分子流体动力学性质的计算机程序。
Biophys J. 1994 Aug;67(2):530-1. doi: 10.1016/S0006-3495(94)80512-0.
2
MULTIHYDRO and MONTEHYDRO: conformational search and Monte Carlo calculation of solution properties of rigid or flexible bead models.MULTIHYDRO和MONTEHYDRO：刚性或柔性珠子模型的构象搜索及溶液性质的蒙特卡罗计算
Biophys Chem. 2005 Jul 1;116(2):121-8. doi: 10.1016/j.bpc.2005.03.005. Epub 2005 Apr 13.
3
Methods and tools for the prediction of hydrodynamic coefficients and other solution properties of flexible macromolecules in solution. A tutorial minireview.方法和工具，用于预测溶液中柔性大分子的流体动力系数和其他溶液性质。教程式综述。
Macromol Biosci. 2010 Jul 7;10(7):721-30. doi: 10.1002/mabi.200900464.
4
SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.
Eur Biophys J. 1997;25(5-6):361-72. doi: 10.1007/s002490050049.
5
Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape.为任意形状的刚性生物粒子构建流体动力学珠-壳模型。
Biophys Chem. 2001 Dec 25;94(3):265-74. doi: 10.1016/s0301-4622(01)00244-7.
6
Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program.使用SOLPRO计算机程序计算珠子模型的核磁共振弛豫、共体积和散射相关特性。
Eur Biophys J. 1999;28(2):119-32. doi: 10.1007/s002490050191.
7
Calculation of the solution properties of flexible macromolecules: methods and applications.柔性大分子溶液性质的计算：方法与应用
Eur Biophys J. 2003 Aug;32(5):477-86. doi: 10.1007/s00249-003-0292-0. Epub 2003 Apr 16.
8
Global fit and structure optimization of flexible and rigid macromolecules and nanoparticles from analytical ultracentrifugation and other dilute solution properties.从分析超速离心和其他稀溶液性质出发，对柔性和刚性大分子及纳米颗粒进行全局拟合和结构优化。
Methods. 2011 May;54(1):115-23. doi: 10.1016/j.ymeth.2010.12.004. Epub 2010 Dec 14.
9
Hydrodynamic modeling: the solution conformation of macromolecules and their complexes.流体动力学建模：大分子及其复合物的溶液构象
Methods Cell Biol. 2008;84:327-73. doi: 10.1016/S0091-679X(07)84012-X.
10
Conformation parameters of linear macromolecules from velocity sedimentation and other hydrodynamic methods.从沉降速度和其他流体力学方法看线型大分子的构象参数。
Methods. 2011 May;54(1):124-35. doi: 10.1016/j.ymeth.2011.02.005. Epub 2011 Feb 12.
引用本文的文献
1
Hydrodynamic properties of macromolecules and nanoparticles in dilute solution: a brief essay on classical and modern concepts.稀溶液中大分子和纳米颗粒的流体动力学性质：关于经典与现代概念的短文
Eur Biophys J. 2025 Aug 24. doi: 10.1007/s00249-025-01791-7.
2
From an obliquely falling rod in a viscous fluid to the motion of suspended magnetic bead chains that are driven by a gradient magnetic field and that make an arbitrary angle with the magnetic force vector: A Stokes flow study.从倾斜落入粘性流体中的棒到由梯度磁场驱动且与磁力向量成任意角度的悬浮磁性珠链的运动：Stokes 流研究。
PLoS One. 2024 Apr 16;19(4):e0301852. doi: 10.1371/journal.pone.0301852. eCollection 2024.
3
Modelling red blood cell optical trapping by machine learning improved geometrical optics calculations.通过机器学习对红细胞光学捕获进行建模改进了几何光学计算。
Biomed Opt Express. 2023 Jun 27;14(7):3748-3762. doi: 10.1364/BOE.488931. eCollection 2023 Jul 1.
4
Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment.核孔复合体的物理学：理论、建模与实验
Phys Rep. 2021 Jul 25;921:1-53. doi: 10.1016/j.physrep.2021.03.003. Epub 2021 Mar 24.
5
Phase Separation of Toxic Dipeptide Repeat Proteins Related to C9orf72 ALS/FTD.与 C9orf72 ALS/FTD 相关的毒性二肽重复蛋白的液-液相分离。
Biophys J. 2020 Aug 18;119(4):843-851. doi: 10.1016/j.bpj.2020.07.005. Epub 2020 Jul 16.
6
Long-Lifetime Metal-Ligand Complexes as Luminescent Probes for DNA.长寿命金属-配体配合物作为DNA的发光探针。
J Fluoresc. 1997 Jun;7(2):107-112. doi: 10.1007/BF02760501.
7
Diffusion Tensors of Arbitrary-Shaped Nanoparticles in Fluid by Molecular Dynamics Simulation.通过分子动力学模拟研究流体中任意形状纳米颗粒的扩散张量
Sci Rep. 2019 Dec 12;9(1):18943. doi: 10.1038/s41598-019-55042-9.
8
The Effect of FG-Nup Phosphorylation on NPC Selectivity: A One-Bead-Per-Amino-Acid Molecular Dynamics Study.FG-Nup 磷酸化对核孔复合物选择性的影响：一个逐氨基酸分子动力学研究。
Int J Mol Sci. 2019 Jan 30;20(3):596. doi: 10.3390/ijms20030596.
9
GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.GRPY：一种用于计算刚性生物大分子流体力学性质的精确珠粒方法。
Biophys J. 2018 Sep 4;115(5):782-800. doi: 10.1016/j.bpj.2018.07.015. Epub 2018 Jul 24.
10
Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1.使用图谱约束的 Langevin 动力学和 NMR 增强域间运动采样：在 Pin1 上的应用。
J Mol Biol. 2018 Jul 6;430(14):2164-2180. doi: 10.1016/j.jmb.2018.05.007. Epub 2018 May 16.
本文引用的文献
1
Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications.复杂、刚性生物大分子的流体动力学性质：理论与应用
Q Rev Biophys. 1981 Feb;14(1):81-139. doi: 10.1017/s0033583500002080.
2
Frictional coefficients of multisubunit structures. I. Theory.多亚基结构的摩擦系数。I. 理论。
Biopolymers. 1967 Feb;5(2):135-48. doi: 10.1002/bip.1967.360050202.
3
Dynamics of fluorescence polarization in macromolecules.大分子中荧光偏振的动力学
Proc Natl Acad Sci U S A. 1972 Jun;69(6):1392-3. doi: 10.1073/pnas.69.6.1392.
Zotero 插件