Literature DB >> 22402497

Computer simulation studies of self-assembling macromolecules.

Wataru Shinoda1, Russell DeVane, Michael L Klein.   

Abstract

Coarse-grained (CG) molecular models are now widely used to understand the structure and functionality of macromolecular self-assembling systems. In the last few years, significant efforts have been devoted to construct quantitative CG models based on data from molecular dynamics (MD) simulations with more detailed all-atom (AA) intermolecular force fields as well as experimental thermodynamic data. We review some of the recent progress pertaining to the MD simulation of self-assembling macromolecular systems, using as illustrations the application of CG models to probe surfactant and lipid self-assembly including liposome and dendrimersome formation as well as the interaction of biomembranes with nanoparticles.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22402497     DOI: 10.1016/j.sbi.2012.01.011

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  15 in total

1.  Biological potential of nanomaterials strongly depends on the suspension media: experimental data on the effects of fullerene C₆₀ on membranes.

Authors:  Barbara Drašler; Damjana Drobne; Nataša Poklar Ulrih; Ajda Ota
Journal:  Protoplasma       Date:  2015-04-02       Impact factor: 3.356

Review 2.  Understanding health and disease with multidimensional single-cell methods.

Authors:  Julián Candia; Jayanth R Banavar; Wolfgang Losert
Journal:  J Phys Condens Matter       Date:  2014-01-22       Impact factor: 2.333

3.  Phenomenology based multiscale models as tools to understand cell membrane and organelle morphologies.

Authors:  N Ramakrishnan; Ravi Radhakrishnan
Journal:  Adv Planar Lipid Bilayers Liposomes       Date:  2015

4.  Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis.

Authors:  Siyoung Kim; Gregory A Voth
Journal:  J Phys Chem B       Date:  2021-06-17       Impact factor: 2.991

5.  Thermodynamic free energy methods to investigate shape transitions in bilayer membranes.

Authors:  N Ramakrishnan; Richard W Tourdot; Ravi Radhakrishnan
Journal:  Int J Adv Eng Sci Appl Math       Date:  2016-01-22

Review 6.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

7.  Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex.

Authors:  Fu-Feng Liu; Bo Huang; Xiao-Yan Dong; Yan Sun
Journal:  PLoS One       Date:  2013-06-12       Impact factor: 3.240

8.  Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation.

Authors:  Christoph Globisch; Venkatramanan Krishnamani; Markus Deserno; Christine Peter
Journal:  PLoS One       Date:  2013-04-16       Impact factor: 3.240

9.  LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry.

Authors:  Jacob D Durrant; Rommie E Amaro
Journal:  PLoS Comput Biol       Date:  2014-07-17       Impact factor: 4.475

10.  Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.

Authors:  Puja Goyal; Hu-Jun Qian; Stephan Irle; Xiya Lu; Daniel Roston; Toshifumi Mori; Marcus Elstner; Qiang Cui
Journal:  J Phys Chem B       Date:  2014-09-16       Impact factor: 2.991

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