Theoretical frameworks for multiscale modeling and simulation

被引：28
作者：
Zhou, Huan-Xiang [1 ,2 ]
机构：
[1] Florida State Univ, Dept Phys, Tallahassee, FL 32306 USA
[2] Florida State Univ, Inst Mol Biophys, Tallahassee, FL 32306 USA
来源：
CURRENT OPINION IN STRUCTURAL BIOLOGY | 2014年 / 25卷
基金：
美国国家卫生研究院;
关键词：
M2 PROTON CHANNEL; MOLECULAR-DYNAMICS SIMULATIONS; INFLUENZA-A VIRUS; BIOMOLECULAR SYSTEMS; ION-TRANSPORT; LIPID-BILAYER; PROTEIN; BINDING; QUANTUM; DNA;
D O I：
10.1016/j.sbi.2014.01.004
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Biomolecular systems have been modeled at a variety of scales, ranging from explicit treatment of electrons and nuclei to continuum description of bulk deformation or velocity. Many challenges of interfacing between scales have been overcome. Multiple models at different scales have been used to study the same system or calculate the same property (e.g., channel conductance). Accurate modeling of biochemical processes under in vivo conditions and the bridging of molecular and subcellular scales will likely soon become reality.
引用
收藏
页码：67 / 76
页数：10
相关论文
共 91 条
[1]   Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion [J].
Ando, Tadashi ;
Skolnick, Jeffrey .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (43) :18457-18462
[2]   Four-scale description of membrane sculpting by BAR domains [J].
Arkhipov, Anton ;
Yin, Ying ;
Schulten, Klaus .
BIOPHYSICAL JOURNAL, 2008, 95 (06) :2806-2821
[3]   Stability and dynamics of virus capsids described by coarse-grained modeling [J].
Arkhipov, Anton ;
Freddolino, Peter L. ;
Schulten, Klaus .
STRUCTURE, 2006, 14 (12) :1767-1777
[4]   Multiscale modeling of biomolecular systems: in serial and in parallel [J].
Ayton, Gary S. ;
Noid, Will G. ;
Voth, Gregory A. .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2007, 17 (02) :192-198
[5]   Membrane remodeling from N-BAR domain interactions: Insights from multi-scale simulation [J].
Ayton, Gary S. ;
Blood, Philip D. ;
Voth, Gregory A. .
BIOPHYSICAL JOURNAL, 2007, 92 (10) :3595-3602
[6]   Systematic multiscale simulation of membrane protein systems [J].
Ayton, Gary S. ;
Voth, Gregory A. .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2009, 19 (02) :138-144
[7]   A microscopic view of ion conduction through the K+ channel [J].
Bernèche, S ;
Roux, B .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (15) :8644-8648
[8]   Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations [J].
Bucher, Denis ;
Hsu, Yuan-Hao ;
Mouchlis, Varnavas D. ;
Dennis, Edward A. ;
McCammon, J. Andrew .
PLOS COMPUTATIONAL BIOLOGY, 2013, 9 (07)
[9]   Diffusion of complex objects embedded in free and supported lipid bilayer membranes: role of shape anisotropy and leaflet structure [J].
Camley, Brian A. ;
Brown, Frank L. H. .
SOFT MATTER, 2013, 9 (19) :4767-4779
[10]   Catalysis of Na+ permeation in the bacterial sodium channel NaVAb [J].
Chakrabarti, Nilmadhab ;
Ing, Christopher ;
Payandeh, Jian ;
Zheng, Ning ;
Catterall, William A. ;
Pomes, Regis .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (28) :11331-11336
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