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Charge Group Partitioning in Biomolecular Simulation

Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
<span title="">2013</span> <i title="Mary Ann Liebert Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/id6xbd2o6fhy7pts2djgwhtmvy" style="color: black;">Journal of Computational Biology</a> </i> &nbsp;
In addition, charge groups are required to have size at most k.  ...  Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level.  ...  ACKNOWLEDGMENTS We thank SARA Computing and Networking Services (www.sara.nl) for their support in using the Lisa Compute Cluster. In addition, we are grateful to the referees for helpful comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/cmb.2012.0239">doi:10.1089/cmb.2012.0239</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23461571">pmid:23461571</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3590896/">pmcid:PMC3590896</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/njp67p5sdjg5xaglwqfffegcya">fatcat:njp67p5sdjg5xaglwqfffegcya</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209023148/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3590896&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/d9/ad/d9ad267c6bebc16b828572878ff3a43a0572a58b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/cmb.2012.0239"> <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/PMC3590896" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

AnNlogNapproximation based on the natural organization of biomolecules for speeding up the computation of long range interactions

Ramu Anandakrishnan, Alexey V. Onufriev
<span title="">2009</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/72zcmi3smndcrdvxgve7ny6ytq" style="color: black;">Journal of Computational Chemistry</a> </i> &nbsp;
Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems.  ...  The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component  ...  The graph on the left shows the partitioning of the whole structure into subunits which are partitioned into groups, which in turn are partitioned into atoms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.21357">doi:10.1002/jcc.21357</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19569183">pmid:19569183</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2818067/">pmcid:PMC2818067</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mxua5dxxgbda3j3irsq7uyneou">fatcat:mxua5dxxgbda3j3irsq7uyneou</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206084751/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2818067&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/15/af/15afe7d9dd6529d85766ee1fbc3eb19b966f16d3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.21357"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818067" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

Ramu Anandakrishnan, Tom R.W. Scogland, Andrew T. Fenley, John C. Gordon, Wu-chun Feng, Alexey V. Onufriev
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rqyaqz3s4neixaio7kt7pdll5q" style="color: black;">Journal of Molecular Graphics and Modelling</a> </i> &nbsp;
Specifically, the electrostatic potential computation, using an analytical linearized Poisson-Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multi-scale method  ...  Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function.  ...  Acknowledgments This work was supported in part by NIH R01 grant GM076121 and by NSF I/UCRC grant IIP-0804155 with support from AMD.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmgm.2010.04.001">doi:10.1016/j.jmgm.2010.04.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20452792">pmid:20452792</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2907926/">pmcid:PMC2907926</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lmxvebf4gvbdbkihn4ajx6hpmm">fatcat:lmxvebf4gvbdbkihn4ajx6hpmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809063545/http://synergy.cs.vt.edu/pubs/papers/ramu-mgm10-surface-potential.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/10/2f/102f9b7f12968d11e9cce26c7966afd22f398bcd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmgm.2010.04.001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907926" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

Jeff Wereszczynski, J. Andrew McCammon
<span title="2011-11-15">2011</span> <i title="Cambridge University Press (CUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jns6cvwyffcm3ojmxntl7de3mu" style="color: black;">Quarterly Reviews of Biophysics (print)</a> </i> &nbsp;
In this review, we discuss how molecular dynamics (MD) simulations may be used in advancing our understanding of the thermodynamics that drive biomolecular recognition.  ...  Molecular recognition plays a central role in biochemical processes.  ...  The polarity of the water molecules also resulted in a charge asymmetry, with a positively charged ligand binding stronger to a negative receptor than a negatively charged ligand binding to a positive  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0033583511000096">doi:10.1017/s0033583511000096</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22082669">pmid:22082669</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3291752/">pmcid:PMC3291752</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vgwyr56fbfhejf5dawnzzxgn5e">fatcat:vgwyr56fbfhejf5dawnzzxgn5e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191118023253/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3291752&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/66/4e/664e43783da1c5f5f41d8c461ab45e8245a1b7ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0033583511000096"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> cambridge.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291752" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6

Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. Van Gunsteren
<span title="">2004</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/72zcmi3smndcrdvxgve7ny6ytq" style="color: black;">Journal of Computational Chemistry</a> </i> &nbsp;
The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6).  ...  Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time.  ...  In particular: Indira Chandrasekhar for the lipid parameters, Roberto Lins for the sugar parameters, and Thereza Soares for the nucleotide parameters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.20090">doi:10.1002/jcc.20090</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15264259">pmid:15264259</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6sp5svronjhf7bptdmk4odusce">fatcat:6sp5svronjhf7bptdmk4odusce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812010125/http://compbio.chemistry.uq.edu.au/mediawiki/upload/3/36/Gromos53a5a6.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/1a/15/1a15a5d2ea884172729facc3a56e5bdbeb50bf77.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.20090"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Biomolecular electrostatics and solvation: a computational perspective

Pengyu Ren, Jaehun Chun, Dennis G. Thomas, Michael J. Schnieders, Marcelo Marucho, Jiajing Zhang, Nathan A. Baker
<span title="">2012</span> <i title="Cambridge University Press (CUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jns6cvwyffcm3ojmxntl7de3mu" style="color: black;">Quarterly Reviews of Biophysics (print)</a> </i> &nbsp;
In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme  ...  behavior) in order to provide a background to understand the different types of solvation models.  ...  Several factors alter the charge state of ionizable groups in a protein : electrostatic interactions between charges of ionizable groups in the same protein, electrostatic interactions between charges  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s003358351200011x">doi:10.1017/s003358351200011x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23217364">pmid:23217364</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3533255/">pmcid:PMC3533255</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f73eg3p3zzh2ncfzk5oyvso3v4">fatcat:f73eg3p3zzh2ncfzk5oyvso3v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308035441/http://pdfs.semanticscholar.org/ec74/78468ef0e5d1ee1ca6cad375f5ef54149f92.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/74/ec7478468ef0e5d1ee1ca6cad375f5ef54149f92.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s003358351200011x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> cambridge.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3533255" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

Daniel J. Cole, Jonah Z. Vilseck, Julian Tirado-Rives, Mike C. Payne, William L. Jorgensen
<span title="2016-04-21">2016</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z2ruvhjfujanbnydakuxtjslca" style="color: black;">Journal of Chemical Theory and Computation</a> </i> &nbsp;
Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical  ...  calculations for use in biomolecular modeling of organic and biomolecular systems.  ...  In fixed-charge MM force fields for condensed-phase simulations, which are the focus of this paper, induction is treated in an effective manner by polarizing the atomic charges.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jctc.6b00027">doi:10.1021/acs.jctc.6b00027</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27057643">pmid:27057643</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4864407/">pmcid:PMC4864407</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4yhfcbv6yvanzczb27trcsv444">fatcat:4yhfcbv6yvanzczb27trcsv444</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170520083212/http://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00027?src=recsys" 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/04/34/043456d16cb230eaaa97ce29f91bd074ae35ddd4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jctc.6b00027"> <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/PMC4864407" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Molecular Mechanics

Kenno Vanommeslaeghe, Olgun Guvench, Alexander D. MacKerell
<span title="2014-05-31">2014</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xtiwjcbzsbd35jtqmz56mrpmb4" style="color: black;">Current pharmaceutical design</a> </i> &nbsp;
Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility.  ...  Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects.  ...  a chemical group having a net charge.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/13816128113199990600">doi:10.2174/13816128113199990600</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23947650">pmid:23947650</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4026342/">pmcid:PMC4026342</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bjeddejtlffrhhee7zjhxczqpe">fatcat:bjeddejtlffrhhee7zjhxczqpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210063435/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4026342&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/4e/ee/4eeec4e3911f4345ab536f678295d46caad4a8f7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/13816128113199990600"> <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/PMC4026342" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

Jens Kleinjung, Walter R. P. Scott, Jane R. Allison, Wilfred F. van Gunsteren, Franca Fraternali
<span title="2012-06-26">2012</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z2ruvhjfujanbnydakuxtjslca" style="color: black;">Journal of Chemical Theory and Computation</a> </i> &nbsp;
Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed.  ...  A simplified representation based on groups of atom types σ g SASA was obtained via partitioning of the atom−type σ i SASA distributions by dynamic programming.  ...  In the GROMOS 43B1 solute force field for in vacuo simulations, this is achieved by adapting the partial charges of groups of atoms that bear a total charge of ±1e, such as in Asp, Glu, Arg, and Lys side  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ct200390j">doi:10.1021/ct200390j</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23180979">pmid:23180979</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3503459/">pmcid:PMC3503459</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hhcnmlizgfdypejwtkoj4d4txy">fatcat:hhcnmlizgfdypejwtkoj4d4txy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211150515/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3503459&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/85/c0/85c045e6794b4ec6143e5cef634461807616b93a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ct200390j"> <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/PMC3503459" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Blue matter on blue gene/L

Robert S. Germain, Blake Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, Michael C. Pitman, Frank Suits, Mark Giampapa, T.J. Christopher Ward
<span title="">2005</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/h4zelo33ojdfzbwajaf5qlthey" style="color: black;">Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis - CODES+ISSS &#39;05</a> </i> &nbsp;
This paper provides an overview of the Blue Matter application development effort within the Blue Gene project that supports our scientific simulation efforts in the areas of protein folding and membrane-protein  ...  In order for an application to exploit the potential of this architecture, the application must scale well to large node counts.  ...  Current practice in biomolecular simulation involves the use of periodic boundary conditions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1084834.1084888">doi:10.1145/1084834.1084888</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/codes/GermainFREPSGW05.html">dblp:conf/codes/GermainFREPSGW05</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lwu5pdkwsjc7fbvtu4zswpkfn4">fatcat:lwu5pdkwsjc7fbvtu4zswpkfn4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200318113834/http://www.cecs.uci.edu/~papers/codes05/PAPERS/2005/CODES_ISSS05/PDFFILES/P207.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/4f/54/4f54896e2caf9c3dcffd42dd06d8233ce565a9c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1084834.1084888"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program

Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel
<span title="2013-11-22">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always contain more than one kind of lipid molecule.  ...  Motivation: Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality  ...  Funding: This research was in part supported by a grant from Biomath Research group at IPM. Conflict of Interest: None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt680">doi:10.1093/bioinformatics/btt680</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24273238">pmid:24273238</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vk5nmffabbh3lewe5oansdzdye">fatcat:vk5nmffabbh3lewe5oansdzdye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728160026/https://watermark.silverchair.com/btt680.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAb0wggG5BgkqhkiG9w0BBwagggGqMIIBpgIBADCCAZ8GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMpfU1JGzdW9ZeFcBmAgEQgIIBcNeHKWXagH1B_FGyaaNJvux7MXUgZHbekT7ZhN5GR0tihnGrDrTIZKzcoiS5uF1d0AnbUQ16Tagbw2ZzPl3aFjv_mz6I7fpvyPjl8fC4bPrJlbqN8zB45OU3jc1vP3p3VSqiEbuh_2Mo__ahJplxQ49wgjsCotLQrMEiF1ZrRvSdpfkXHWVm6AGQHz_CgOtxwB5qIgl9lNKtR3Ddq2r6dw8GZv909kusDMo8c7DBI0FwXKHk7QtfgPn_Y4sGmexuZCsLIv7VbUoZvE5tmEjBIEHUSVOMcIFBIrgKUfzSpjw4ezpcCWYwvMqODOFqSW3w6177F65jVM3P95eIUJPtI_8QS-lgQM6BUMczLIXtCwVL5bbFsLT-8kh-g8vt-miIru4Iby3KAZdnzxGQzZPxenzcit4BO-5Cm0Yz9Dc82LpJ7dHquLDt0dC9dxImLhK7usdMJLib3GaC6RejxVUynHxnP9hicEKewA3xLN_pzr6Q" 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/1c/37/1c370750f9049917093ab3272bbb51e0e7c0ff71.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt680"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

First principles characterisation of bio–nano interface

Ian Rouse, David Power, Erik G. Brandt, Matthew Schneemilch, Konstantinos Kotsis, Nick Quirke, Alexander P. Lyubartsev, Vladimir Lobaskin
<span title="2021-06-10">2021</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/knc3mgis4rdntku3ubqh4roxhu" style="color: black;">Physical Chemistry, Chemical Physics - PCCP</a> </i> &nbsp;
simulations, the OH-groups were attached to Ti surface atoms in a random manner.  ...  Each hydroxyl group contributes a charge of about À0.4e (taking in mind than if an OH group is attached to undercoordinated Ti-O5 atom, its force field type is changed to Ti-O6).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/d1cp01116b">doi:10.1039/d1cp01116b</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34109956">pmid:34109956</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vgovz7hepbau5kb6g4icrmvlqq">fatcat:vgovz7hepbau5kb6g4icrmvlqq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715011838/https://pubs.rsc.org/en/content/articlepdf/2021/cp/d1cp01116b" 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/db/f6/dbf66e50f6e39613c28b26c0c2287c714be61654.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/d1cp01116b"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Interactions between Phase-Separated Liquids and Membrane Surfaces

Samuel Botterbusch, Tobias Baumgart
<span title="2021-01-31">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/smrngspzhzce7dy6ofycrfxbim" style="color: black;">Applied Sciences</a> </i> &nbsp;
However, membranes are ubiquitous throughout cells, and many biomolecular condensates interact with membrane surfaces.  ...  We summarize the common phenomena that arise in these systems of liquid phases and membranes.  ...  This model builds on Semenov and Rubenstein's mean-field theory for associative polymers [24] , defining "sticker" regions as groups that engage in attractive interactions and "spacers" as parts of the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/app11031288">doi:10.3390/app11031288</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34327010">pmid:34327010</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8315427/">pmcid:PMC8315427</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cwj2hfrrgbecbasisnrpa54yre">fatcat:cwj2hfrrgbecbasisnrpa54yre</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210209094621/https://res.mdpi.com/d_attachment/applsci/applsci-11-01288/article_deploy/applsci-11-01288-v3.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/8c/16/8c165ee17992db27b96aa214daf7c910ac1130f7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/app11031288"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8315427" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

Alessandra Villa, Alan E. Mark
<span title="2002-04-04">2002</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/72zcmi3smndcrdvxgve7ny6ytq" style="color: black;">Journal of Computational Chemistry</a> </i> &nbsp;
The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations using molecular dynamics simulations  ...  The dependence of the calculated free energies on the atomic partial charges was also studied.  ...  Acknowledgments The authors wish in particular to thank B. Hess (University of Groningen) and H. J. C.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.10052">doi:10.1002/jcc.10052</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11948581">pmid:11948581</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mdl2kkatgfgwlj76nygywjvbcm">fatcat:mdl2kkatgfgwlj76nygywjvbcm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170219215453/http://compbio.biosci.uq.edu.au/mediawiki/upload/8/83/AM_02_01.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/be/cf/becf8cabf5e9d78de99167a34d52dc16d53df159.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.10052"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning

Louis P. Lee, Daniel J. Cole, Chris-Kriton Skylaris, William L. Jorgensen, Mike C. Payne
<span title="2013-06-25">2013</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z2ruvhjfujanbnydakuxtjslca" style="color: black;">Journal of Chemical Theory and Computation</a> </i> &nbsp;
Atomic partial charges for use in traditional force fields for biomolecular simulation are often fit to the electrostatic potentials of small molecules and, hence, neglect large-scale electronic polarization  ...  Simulated NMR data derived from molecular dynamics of three proteins using force fields based on the ONETEP charges are in good agreement with experiment.  ...  ■ ACKNOWLEDGMENTS We are grateful to Nicholas Hine for ONETEP-related technical consultations and to Greg Lever for bulk water simulations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ct400279d">doi:10.1021/ct400279d</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23894231">pmid:23894231</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3719162/">pmcid:PMC3719162</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jgq6kq5pyfgrzbn7x22ob3yybi">fatcat:jgq6kq5pyfgrzbn7x22ob3yybi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210001531/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3719162&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/24/fc/24fcb810b35e13733eeb8e9bfa53a84ff05e3c5a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ct400279d"> <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/PMC3719162" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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