@article{koivuniemi_revealing_2012,
title = {Revealing structural and dynamical properties of high density lipoproteins through molecular simulations},
volume = {8},
url = {http://dx.doi.org/10.1039/C1SM06742G},
doi = {10.1039/C1SM06742G},
abstract = {The structure and function of high density lipoprotein {(HDL)} particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of {HDL.} Further, because of the complex composition of {HDL}, understanding the impact of its structure and dynamics on the function of {HDL} in reverse cholesterol transport has also been a major issue. Recent progress in molecular simulation methodology and computing power has made a difference, as it has enabled essentially atomistic considerations of {HDL} particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of {HDL} particles as revealed by atomistic and coarse-grained molecular dynamics simulations. We present examples which demonstrate how simulations and experiments can be carried out in unison, showing the added value that emerges from this interplay. We also discuss the possibilities that simulations could offer to better understand the complex phenomena associated with {HDL}, the goal being to understand its function.},
number = {5},
journal = {Soft Matter},
author = {Koivuniemi, Artturi and Vattulainen, Ilpo},
year = {2012},
pages = {1262--1267}
}
@article{huang_apolipoprotein_2011,
title = {Apolipoprotein {A-I} structural organization in high-density lipoproteins isolated from human plasma},
volume = {18},
issn = {1545-9993},
url = {http://dx.doi.org/10.1038/nsmb.2028},
doi = {10.1038/nsmb.2028},
number = {4},
journal = {Nature Structural {\&} Molecular Biology},
author = {Huang, Rong and Silva, R A Gangani D and Jerome, W Gray and Kontush, Anatol and Chapman, M John and Curtiss, Linda K and Hodges, Timothy J and Davidson, W Sean},
year = {2011},
pages = {416--422},
}
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title = {Role of lipids in spheroidal high density lipoproteins},
volume = {6},
number = {10},
journal = {{PLoS} computational biology},
author = {Vuorela, T. and Catte, A. and Niemelä, {P.S.} and Hall, A. and Hyvönen, {M.T.} and Marrink, {S.J.} and Karttunen, M. and Vattulainen, I.},
year = {2010},
pages = {e1000964},
}
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title={Interfacial tension and surface pressure of high density lipoprotein, low density lipoprotein, and related lipid droplets},
author={Ollila, OH and Lamberg, Antti and Lehtivaara, Maria and Koivuniemi, Artturi and Vattulainen, Ilpo},
journal={Biophysical journal},
volume={103},
number={6},
pages={1236--1244},
year={2012},
publisher={Elsevier}
}
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title={Introduction to molecular dynamics simulation},
author={Allen, Michael P},
journal={Computational Soft Matter: From Synthetic Polymers to Proteins},
volume={23},
pages={1--28},
year={2004},
publisher={NIC Series}
}
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author = {Eisenhaber, Frank and Lijnzaad, Philip and Argos, Patrick and Sander, Chris and Scharf, Michael},
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%%
%% The primary VMD citation, should be used by all publications using VMD
%%
@article{HUMP96,
author={William Humphrey and Andrew Dalke and Klaus Schulten},
title={{VMD} -- {V}isual {M}olecular {D}ynamics},
journal={Journal of Molecular Graphics},
year=1996,
volume=14,
pages={33-38},
number={1},
tbstatus={Published.},
techrep={},
tbreference={222}
}
%%
%% Interactive Molecular Dynamics, cited by papers doing IMD simulations
%%
@inproceedings{STON2001,
author={John Stone and Justin Gullingsrud and Paul Grayson and Klaus Schulten},
title={A system for interactive molecular dynamics simulation},
booktitle={2001 ACM Symposium on Interactive 3D Graphics},
publisher={ACM SIGGRAPH},
address={New York},
editor={John F. Hughes and Carlo H. S\'equin},
pages={191-194},
year={2001},
note={},
tbreference={304},
tbstatus={Published.},
annote={This symposium took place between March 19-21, 2001. {ISBN} 1-58113-292-1.}
}
%%
%% The primary VMD citation, should be used by all publications using VMD
%%
@article{HUMP96,
author={William Humphrey and Andrew Dalke and Klaus Schulten},
title={{VMD} -- {V}isual {M}olecular {D}ynamics},
journal={Journal of Molecular Graphics},
year=1996,
volume=14,
pages={33-38},
note={},
tbstatus={Published.},
techrep={},
tbreference={222}
}
%%
%% Tachyon ray tracing library (built-into VMD and/or distributed with VMD)
%% Please cite Tachyon if you use it to make figures within VMD.
%%
@mastersthesis{STON1998,
author = {John Stone},
title = "{\em An Efficient Library for Parallel Ray Tracing and Animation}",
school = "Computer Science Department, University of Missouri-Rolla",
year = {1998}
}
%%
%% STRIDE Secondary Structure Prediction (distributed with VMD)
%%
%% Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
%% assignment. Proteins: structure, function and genetics, 23, 566-579.
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author={D. Frishman and P. Argos},
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pages={566-579},
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note={},
annote={}
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volume = {111},
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number = {5},
journal = {Circulation}}
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title = {High Density Lipoproteins and Arteriosclerosis: Role of Cholesterol Efflux and Reverse Cholesterol Transport},
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volume = {21},
pages = {13--27},
number = {1},
journal = {Arteriosclerosis, Thrombosis, and Vascular Biology}}
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author = {Ohashi, R.},
title = {Reverse cholesterol transport and cholesterol efflux in atherosclerosis},
year = {2005},
volume = {98},
pages = {845--856},
number = {12}}
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author = "AntiSense",
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year = "2010",
note = "Viitattu: 01.12.2014",
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year = "2016",
note = "Viitattu: 10.05.2016",
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@article{Vermeer2007,
abstract = {{Order parameters from deuterium NMR are often used to validate or calibrate molecular dynamics simulations. This paper gives a short overview of the literature in which experimental order parameters from (2)H NMR are compared to those calculated from MD simulations. The different ways in which order parameters from experiment are used to calibrate and validate simulations are reviewed. In the second part of this review, a case study of cholesterol in a DMPC bilayer is presented. It is concluded that the agreement between experimental data and simulation is favorable in the hydrophobic region of the membrane, for both the phospholipids and cholesterol. In the interfacial region the agreement is less satisfactory, probably because of the high polarity of this region which makes the correct computation of the electrostatics more complex.}},
author = {Vermeer, Louic S. and de Groot, Bert L. and R\'{e}at, Val\'{e}rie and Milon, Alain and Czaplicki, Jerzy},
booktitle = {European Biophysics Journal},
citeulike-article-id = {2599289},
citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00249-007-0192-9},
citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17598103},
citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17598103},
citeulike-linkout-3 = {http://www.springerlink.com/content/wn61880407618j11},
day = {1},
doi = {10.1007/s00249-007-0192-9},
issn = {0175-7571},
journal = {European biophysics journal},
keywords = {lipids},
number = {8},
pages = {919--931},
pmid = {17598103},
posted-at = {2014-09-16 21:11:45},
priority = {2},
title = {{Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments.}},
url = {http://dx.doi.org/10.1007/s00249-007-0192-9},
volume = {36},
year = {2007}
}
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author = {Heikkilä, Elena and Gurtovenko, Andrey A. and Martinez-Seara, Hector and Häkkinen, Hannu and Vattulainen, Ilpo and Akola, Jaakko},
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year = {2012},
volume = {116},
pages = {9805--9815},
file = {FULLTEXT:/srv/http/kirjasto/library/00031.pdf:PDF}
}
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note = "",
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url = "http://www.sciencedirect.com/science/article/pii/S0378517310001857",
author = "Wen-Li Zhang and Xiao Gu and Hui Bai and Ru-Hui Yang and Chen-Dong Dong and Jian-Ping Liu",
}
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author = {O. Tange},
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author={S. van der Walt and S. C. Colbert and G. Varoquaux},
journal={Computing in Science Engineering},
title={The NumPy Array: A Structure for Efficient Numerical Computation},
year={2011},
volume={13},
number={2},
pages={22-30},
keywords={data structures;high level languages;mathematics computing;numerical analysis;Python programming language;high level language;numerical computation;numerical data;numpy array;Arrays;Computational efficiency;Finite element methods;Numerical analysis;Performance evaluation;Resource management;Vector quantization;NumPy;Python;numerical computations;programming libraries;scientific programming},
doi={10.1109/MCSE.2011.37},
ISSN={1521-9615},
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