Protein-Ligand Binding Simulation with the Martini Coarse-Grained Force Field

被引:1
|
作者
Negami, Tatsuki [1 ]
Shimizu, Kentaro [1 ]
Terada, Tohru [1 ]
机构
[1] Univ Tokyo, Tokyo, Japan
关键词
D O I
10.1016/j.bpj.2013.11.3370
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
引用
收藏
页码:609A / 609A
页数:1
相关论文
共 50 条
  • [31] A Coarse-Grained MARTINI-Like Force Field for DNA Unzipping in Nanopores
    Stachiewicz, Anna
    Molski, Andrzej
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2015, 36 (13) : 947 - 956
  • [32] Martini 3: a general purpose force field for coarse-grained molecular dynamics
    Paulo C. T. Souza
    Riccardo Alessandri
    Jonathan Barnoud
    Sebastian Thallmair
    Ignacio Faustino
    Fabian Grünewald
    Ilias Patmanidis
    Haleh Abdizadeh
    Bart M. H. Bruininks
    Tsjerk A. Wassenaar
    Peter C. Kroon
    Josef Melcr
    Vincent Nieto
    Valentina Corradi
    Hanif M. Khan
    Jan Domański
    Matti Javanainen
    Hector Martinez-Seara
    Nathalie Reuter
    Robert B. Best
    Ilpo Vattulainen
    Luca Monticelli
    Xavier Periole
    D. Peter Tieleman
    Alex H. de Vries
    Siewert J. Marrink
    Nature Methods, 2021, 18 : 382 - 388
  • [33] Coarse-Grained Modeling of DNA-Vesicle Systems with the Martini Force Field
    Uusitalo, Jaakko
    Ingolfsson, Helgi I.
    Akhshi, Parisa
    Tieleman, D. Peter
    Poolman, Bert
    Herrmann, Andreas
    Marrink, Siewert J.
    BIOPHYSICAL JOURNAL, 2014, 106 (02) : 803A - 803A
  • [34] Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field
    Gautieri, Alfonso
    Russo, Antonio
    Vesentini, Simone
    Redaelli, Alberto
    Buehler, Markus J.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (04) : 1210 - 1218
  • [35] Martini 3: a general purpose force field for coarse-grained molecular dynamics
    Souza, Paulo C. T.
    Alessandri, Riccardo
    Barnoud, Jonathan
    Thallmair, Sebastian
    Faustino, Ignacio
    Grunewald, Fabian
    Patmanidis, Ilias
    Abdizadeh, Haleh
    Bruininks, Bart M. H.
    Wassenaar, Tsjerk A.
    Kroon, Peter C.
    Melcr, Josef
    Nieto, Vincent
    Corradi, Valentina
    Khan, Hanif M.
    Domanski, Jan
    Javanainen, Matti
    Martinez-Seara, Hector
    Reuter, Nathalie
    Best, Robert B.
    Vattulainen, Ilpo
    Monticelli, Luca
    Periole, Xavier
    Tieleman, D. Peter
    de Vries, Alex H.
    Marrink, Siewert J.
    NATURE METHODS, 2021, 18 (04) : 382 - +
  • [36] Protein-ligand binding with Martini 3
    Marrink, Siewert
    BIOPHYSICAL JOURNAL, 2023, 122 (03) : 325A - 325A
  • [37] A Structurally Flexible Protein Backbone for the MARTINI Coarse Grained Force Field
    Periole, Xavier
    Marrink, Siewert-Jan
    Tieleman, Peter
    BIOPHYSICAL JOURNAL, 2011, 100 (03) : 613 - 613
  • [38] Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simblations with Implicit Solvent
    Arnarez, Clement
    Uusitalo, Jaakko J.
    Masman, Marcelo F.
    Ingolfsson, Helgi I.
    de Jong, Djurre H.
    Melo, Manuel N.
    Periole, Xavier
    de Vries, Alex H.
    Marrink, Siewert J.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2015, 11 (01) : 260 - 275
  • [39] Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding
    Negami, Tatsuki
    Shimizu, Kentaro
    Terada, Tohru
    CHEMICAL PHYSICS LETTERS, 2020, 742
  • [40] Coarse-grained Simulation using Multipolar Force Field Model
    Chiu, Shuo-Feng
    Chao, Sheng D.
    PROCEEDINGS OF 4TH IEEE INTERNATIONAL CONFERENCE ON APPLIED SYSTEM INNOVATION 2018 ( IEEE ICASI 2018 ), 2018, : 1188 - 1191