Filters








6,306 Hits in 9.5 sec

Membrane Permeability in Biological Systems: A Systems Biology Perspective

Shailza Singh
<span title="">2011</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cfj7yw2qavhc5f35je6wes764m" style="color: black;">Journal of computer science and systems biology</a> </i> &nbsp;
It is thus particularly encouraging to revisit the force field parameterization on the basis of extended QM calculations (structures, energetics and phase transitions) in conjunction with available experimental  ...  A full understanding of biological function emerges only if we are able to integrate all relevant information at multiple levels of organization to recreate dynamic interactions.  ...  In the case of lipid membranes, both all-atom and united atom force field have been used [24] . There are several possibilities to treat polarisability explicitly in the force field calculations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jcsb.1000072">doi:10.4172/jcsb.1000072</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/njehji5i5fhujiebgfniz5b6u4">fatcat:njehji5i5fhujiebgfniz5b6u4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817050104/https://www.omicsonline.org/membrane-permeability-in-biological-systems-a-systems-biology-perspective-jcsb.1000027.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d3/73/d3739e7a7c21edf5959b13b1cfb6843aed957a53.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jcsb.1000072"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

LIPID11: A Modular Framework for Lipid Simulations Using Amber

Åge A. Skjevik, Benjamin D. Madej, Ross C. Walker, Knut Teigen
<span title="2012-09-04">2012</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ah52wn6qqbeilcx7mb5h3ozbeu" style="color: black;">Journal of Physical Chemistry B</a> </i> &nbsp;
Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF).  ...  Our findings suggest that LIPID11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field.  ...  Of the major published force fields for lipid simulation the most widely used all-atom variants are the Charmm force fields, 14−17 the latest of which can reproduce a range of lipid bilayer experimental  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/jp3059992">doi:10.1021/jp3059992</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22916730">pmid:22916730</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3771533/">pmcid:PMC3771533</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ftdvoeghxbbztloqbiozwlp44i">fatcat:ftdvoeghxbbztloqbiozwlp44i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140818023043/http://www.rosswalker.co.uk/papers/2012_JPCB_Lipid11.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7d/ee/7deead3fe1b832402d1247faafde161a09378eba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/jp3059992"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771533" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Coarse-grained Molecular Dynamics of lipid bilayer membranes with multiple components

Peng Chen, Vivek Shenoy
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ...  The multiscale development involves, (1) coarse graining via implicit solvent using Langevin equation, and (2) that of atomistic potential function onto residue-scale force field via our REACH method.  ...  For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2059">doi:10.1016/j.bpj.2008.12.2059</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fsmrkqedbnbn5o5y2mmc3evr3e">fatcat:fsmrkqedbnbn5o5y2mmc3evr3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170928220857/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/6e0/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTUwODAyMjc5MA%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3c/b3/3cb3597be87e9cdb8293a7c0c3dba08d040a6ef6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2059"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Improved Coarse Grained Force-Field Parameters for Biomembranes

See-Wing Chiu, Eric Jakobsson, H. Larry Scott
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ...  The multiscale development involves, (1) coarse graining via implicit solvent using Langevin equation, and (2) that of atomistic potential function onto residue-scale force field via our REACH method.  ...  For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2057">doi:10.1016/j.bpj.2008.12.2057</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fzo4bpxrvfgd7ged53gh5gvb44">fatcat:fzo4bpxrvfgd7ged53gh5gvb44</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303153746/https://core.ac.uk/download/pdf/82748633.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2b/06/2b06ba8ceab1feb1b270190c03074838b063da08.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2057"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Multiscale Simulation of Nucleation-limited Viral Capsid Assembly

Navodit Misra, Russell Schwartz
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ...  The multiscale development involves, (1) coarse graining via implicit solvent using Langevin equation, and (2) that of atomistic potential function onto residue-scale force field via our REACH method.  ...  For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2056">doi:10.1016/j.bpj.2008.12.2056</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i2kllxpalrfbjfeksfpriqjdsi">fatcat:i2kllxpalrfbjfeksfpriqjdsi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190417154739/https://core.ac.uk/download/pdf/82299604.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/da/14/da14228b6cd9459d86e54c35735c605d6ea435fe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2056"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Hierarchical Reduction Method of Protein Structures for Understanding Protein Dynamics

Jae In Kim, Gwonchan Yoon, Sungsoo Na, Kilho Eom
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ...  The multiscale development involves, (1) coarse graining via implicit solvent using Langevin equation, and (2) that of atomistic potential function onto residue-scale force field via our REACH method.  ...  For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2058">doi:10.1016/j.bpj.2008.12.2058</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7qkzs7zfdvhxfmfvbgnlq4n66m">fatcat:7qkzs7zfdvhxfmfvbgnlq4n66m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190327114102/https://core.ac.uk/download/pdf/82049822.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/94/42/9442c4dbca98512cfe101ba6bc9bc37935c202da.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2058"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Coarse Graining Methodology for the Multiscale Simulation of Complex Biological Systems

Kei Moritsugu, Jeremy C. Smith, Akinori Kidera
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ...  The multiscale development involves, (1) coarse graining via implicit solvent using Langevin equation, and (2) that of atomistic potential function onto residue-scale force field via our REACH method.  ...  For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2055">doi:10.1016/j.bpj.2008.12.2055</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4s4tnxo6ofhipby2gvl2d2plt4">fatcat:4s4tnxo6ofhipby2gvl2d2plt4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922153918/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/036/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTUwODAyMjc1Mw%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b6/65/b66581892e3ae2232b03ed87e0747700242bcfaf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2055"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field

Benjamin D. Madej, Ian R. Gould, Ross C. Walker
<span title="2015-09-11">2015</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ah52wn6qqbeilcx7mb5h3ozbeu" style="color: black;">Journal of Physical Chemistry B</a> </i> &nbsp;
The General Amber and Lipid14 force fields are used as a basis for assigning atom types and basic parameters.  ...  The Amber Lipid14 force field is expanded to include cholesterol parameters for all-atom cholesterol and lipid bilayer molecular dynamics simulations.  ...  I.R.G. also acknowledges funding from the EU in the form of the project "HeCaToS -Hepatic and Cardiac Toxicity Systems modeling" FP7-HEALTH-2013-INNOVATION-1 (Project number 602156).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jpcb.5b04924">doi:10.1021/acs.jpcb.5b04924</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26359797">pmid:26359797</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5079186/">pmcid:PMC5079186</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a66zbouljrdrbo3ubr6rxhez4i">fatcat:a66zbouljrdrbo3ubr6rxhez4i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206083231/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5079186&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ed/73/ed73b6a8cd2bcbe6afcbd6568f3c8d083a2ff532.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jpcb.5b04924"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079186" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields

Åge A. Skjevik, Benjamin D. Madej, Callum J. Dickson, Knut Teigen, Ross C. Walker, Ian R. Gould
<span title="">2015</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eb2lcnpf2zeezkmfckcvxw2pgi" style="color: black;">Chemical Communications</a> </i> &nbsp;
In this work we report the first example of spontaneous lipid bilayer formation in unbiased all-atom molecular dynamics (MD) simulations.  ...  The self-assembly simulations in the present work employ all-atom representations using the recently published AMBER Lipid14 force field 11 as well as the CHARMM36 force field for lipids (C36). 12 Lipid14  ...  A more comprehensive study of selfassembly using several all-atom force fields, a broader selection of lipid types as well as mixtures of proteins with lipids will form the basis of future work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4cc09584g">doi:10.1039/c4cc09584g</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25679020">pmid:25679020</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5084445/">pmcid:PMC5084445</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b4fgregegjgfldxbnvf3rlfrlq">fatcat:b4fgregegjgfldxbnvf3rlfrlq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810114018/http://www.rosswalker.co.uk/papers/2015_02_Skjevik_Walker_Chem_Comm_Lipid_Self_Assembly_c4cc09584g.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/06/30/06308b1c895c0dfd0d06829bdad7a88acf66af17.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4cc09584g"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5084445" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prediction of Membrane Binding, Orientation and Permeability of Peptide-like Molecules Using a Continuum Model of the Lipid Bilayer

Andrei L. Lomize, Irina D. Pogozheva, Shaomeng Wang, Henry I. Mosberg
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ...  The multiscale development involves, (1) coarse graining via implicit solvent using Langevin equation, and (2) that of atomistic potential function onto residue-scale force field via our REACH method.  ...  For united-atom model, we have recently shown this from-the-ground-up derived force fields for the hydrocarbons and the smaller organic compounds are completely transferable to simulation of phospholipid  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2060">doi:10.1016/j.bpj.2008.12.2060</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jqvzysyypbaepofi67eniprdzm">fatcat:jqvzysyypbaepofi67eniprdzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190417055007/https://core.ac.uk/download/pdf/82050083.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/01/fe01086ee10b24ee5856ca5a1b74d3b539e00956.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2060"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Sugar-Membrane Interactions: An All-Atom Replica Exchange Molecular Dynamics Study of a Virulent Factor from tb

Jianhui Tian, Parthasarathi Ramakrishnan S. Gnanakaran
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
The requirements on disk space, input/output (I/O) and data transfer bandwidth are excessively high due to the large volume, possibly terabytes or petabytes, of data generated.  ...  Storage of large molecular dynamics (MD) simulation measurements in standard databases is a challenging task.  ...  Here, we conduct constant pressure all-atom replica exchange molecular dynamics simulations using CHARMM c36 force field to understand the interaction between di-mannose and membrane.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2874">doi:10.1016/j.bpj.2010.12.2874</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w7y7obwrejcylks5yy6ysvhd5e">fatcat:w7y7obwrejcylks5yy6ysvhd5e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171003142628/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/cd3/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTUxMDA0Mzc3OA%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6e/7c/6e7c808a3bf9bcd725b05f3e944e8b419f5eef6e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2874"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Label-free characterization of biomembranes: from structure to dynamics

Alireza Mashaghi, Samaneh Mashaghi, Ilya Reviakine, Ron M. A. Heeren, Vahid Sandoghdar, Mischa Bonn
<span title="">2014</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qoebttzoxbfgviecxmhjrua4eu" style="color: black;">Chemical Society Reviews</a> </i> &nbsp;
We review recent progress in the study of the structure and dynamics of phospholipid membranes and associated proteins, using novel label-free analytical tools.  ...  Recent advances in applying such techniques to biological and model membranes for biophysical studies and biosensing applications are presented, and future prospects are discussed.  ...  Acknowledgements The authors are grateful to Dr Sapun Parekh for critical reading of the manuscript and Dr Andreas Engel for discussions. Notes and references  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c3cs60243e">doi:10.1039/c3cs60243e</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24253187">pmid:24253187</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t33457rl4fcubdd4jt4cv5w3hq">fatcat:t33457rl4fcubdd4jt4cv5w3hq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430214229/https://pubs.rsc.org/en/content/articlepdf/2014/cs/c3cs60243e" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/32/b6/32b6463a909077f5366c384639b106a891c13772.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c3cs60243e"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Refining and Testing CHARMM Lipid Parameters for Biologically Important Membranes

Joseph B. Lim, Jeffery B. Klauda
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
The requirements on disk space, input/output (I/O) and data transfer bandwidth are excessively high due to the large volume, possibly terabytes or petabytes, of data generated.  ...  Storage of large molecular dynamics (MD) simulation measurements in standard databases is a challenging task.  ...  Here, we conduct constant pressure all-atom replica exchange molecular dynamics simulations using CHARMM c36 force field to understand the interaction between di-mannose and membrane.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2871">doi:10.1016/j.bpj.2010.12.2871</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dosvmiiwrbcspl6u46eggp27b4">fatcat:dosvmiiwrbcspl6u46eggp27b4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170925025758/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/20f/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTUxMDA0Mzc0Mg%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/96/8e968bc934720a2ad1b40cea8d2efa5754d6ff3d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2871"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Molecular Modeling of Membrane Interactions with Trehalose - A Molecular View on the Water Replacement Hypothesis

Elena Golovina, Andrey Golovin, Roland Faller
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
The requirements on disk space, input/output (I/O) and data transfer bandwidth are excessively high due to the large volume, possibly terabytes or petabytes, of data generated.  ...  Storage of large molecular dynamics (MD) simulation measurements in standard databases is a challenging task.  ...  Here, we conduct constant pressure all-atom replica exchange molecular dynamics simulations using CHARMM c36 force field to understand the interaction between di-mannose and membrane.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2875">doi:10.1016/j.bpj.2010.12.2875</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p2ok3tuyfjgebbsdjhepjdrpse">fatcat:p2ok3tuyfjgebbsdjhepjdrpse</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190414181156/https://core.ac.uk/download/pdf/82628266.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b5/cd/b5cdd90f36442140d55074999296ec218ab22fc4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2875"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Data Compression for Molecular Simulations

Anand Kumar, Xingquan Zhu, Yi-Cheng Tu, Sagar A. Pandit
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
The requirements on disk space, input/output (I/O) and data transfer bandwidth are excessively high due to the large volume, possibly terabytes or petabytes, of data generated.  ...  Storage of large molecular dynamics (MD) simulation measurements in standard databases is a challenging task.  ...  Here, we conduct constant pressure all-atom replica exchange molecular dynamics simulations using CHARMM c36 force field to understand the interaction between di-mannose and membrane.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2870">doi:10.1016/j.bpj.2010.12.2870</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wwxglhzbgze4lm4p4huxwffgpq">fatcat:wwxglhzbgze4lm4p4huxwffgpq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190418064243/https://core.ac.uk/download/pdf/82393830.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ec/52/ec52c72d347c612b1deebc73bc9de54ea1777475.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2010.12.2870"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 6,306 results