200 related articles for article (PubMed ID: 31059255)
41. Coarse-grained dynamic RNA titration simulations.
Pasquali S; Frezza E; Barroso da Silva FL
Interface Focus; 2019 Jun; 9(3):20180066. PubMed ID: 31065339
[TBL] [Abstract][Full Text] [Related]
42. Assessing the Quality of the OPEP Coarse-Grained Force Field.
Barducci A; Bonomi M; Derreumaux P
J Chem Theory Comput; 2011 Jun; 7(6):1928-34. PubMed ID: 26596453
[TBL] [Abstract][Full Text] [Related]
43. Coarse-grained model of proteins incorporating atomistic detail of the active site.
Neri M; Anselmi C; Cascella M; Maritan A; Carloni P
Phys Rev Lett; 2005 Nov; 95(21):218102. PubMed ID: 16384187
[TBL] [Abstract][Full Text] [Related]
44. Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation.
Shi C; Wallace JA; Shen JK
Biophys J; 2012 Apr; 102(7):1590-7. PubMed ID: 22500759
[TBL] [Abstract][Full Text] [Related]
45. Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization.
van Teijlingen A; Swanson HWA; Lau KHA; Tuttle T
J Phys Chem Lett; 2022 May; 13(18):4046-4051. PubMed ID: 35486900
[TBL] [Abstract][Full Text] [Related]
46. Constant-pH molecular dynamics using continuous titration coordinates.
Lee MS; Salsbury FR; Brooks CL
Proteins; 2004 Sep; 56(4):738-52. PubMed ID: 15281127
[TBL] [Abstract][Full Text] [Related]
47. Why are coarse-grained force fields too fast? A look at dynamics of four coarse-grained polymers.
Depa P; Chen C; Maranas JK
J Chem Phys; 2011 Jan; 134(1):014903. PubMed ID: 21219026
[TBL] [Abstract][Full Text] [Related]
48. A coarse-grained protein force field for folding and structure prediction.
Maupetit J; Tuffery P; Derreumaux P
Proteins; 2007 Nov; 69(2):394-408. PubMed ID: 17600832
[TBL] [Abstract][Full Text] [Related]
49. Coarse-grained model of titrating peptides interacting with lipid bilayers.
Tesei G; Vazdar M; Lund M
J Chem Phys; 2018 Dec; 149(24):244108. PubMed ID: 30599743
[TBL] [Abstract][Full Text] [Related]
50. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.
Wallace JA; Shen JK
J Chem Phys; 2012 Nov; 137(18):184105. PubMed ID: 23163362
[TBL] [Abstract][Full Text] [Related]
51. Chain dynamics of poly(ethylene-alt-propylene) melts by means of coarse-grained simulations based on atomistic molecular dynamics.
Pérez-Aparicio R; Colmenero J; Alvarez F; Padding JT; Briels WJ
J Chem Phys; 2010 Jan; 132(2):024904. PubMed ID: 20095706
[TBL] [Abstract][Full Text] [Related]
52. An overview of molecular dynamics simulations of oxidized lipid systems, with a comparison of ELBA and MARTINI force fields for coarse grained lipid simulations.
Siani P; de Souza RM; Dias LG; Itri R; Khandelia H
Biochim Biophys Acta; 2016 Oct; 1858(10):2498-2511. PubMed ID: 27058982
[TBL] [Abstract][Full Text] [Related]
53. Efficient implementation of constant pH molecular dynamics on modern graphics processors.
Arthur EJ; Brooks CL
J Comput Chem; 2016 Sep; 37(24):2171-80. PubMed ID: 27405884
[TBL] [Abstract][Full Text] [Related]
54. Translational mobilities of proteins in nanochannels: A coarse-grained molecular dynamics study.
Haridasan N; Kannam SK; Mogurampelly S; Sathian SP
Phys Rev E; 2018 Jun; 97(6-1):062415. PubMed ID: 30011556
[TBL] [Abstract][Full Text] [Related]
55. Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins.
Poma AB; Cieplak M; Theodorakis PE
J Chem Theory Comput; 2017 Mar; 13(3):1366-1374. PubMed ID: 28195464
[TBL] [Abstract][Full Text] [Related]
56. Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?
Machuqueiro M; Baptista AM
Proteins; 2011 Dec; 79(12):3437-47. PubMed ID: 22072522
[TBL] [Abstract][Full Text] [Related]
57. Necessity of high-resolution for coarse-grained modeling of flexible proteins.
Jia Z; Chen J
J Comput Chem; 2016 Jul; 37(18):1725-33. PubMed ID: 27130454
[TBL] [Abstract][Full Text] [Related]
58. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.
Riniker S; van Gunsteren WF
J Chem Phys; 2011 Feb; 134(8):084110. PubMed ID: 21361530
[TBL] [Abstract][Full Text] [Related]
59. pKa values in proteins determined by electrostatics applied to molecular dynamics trajectories.
Meyer T; Knapp EW
J Chem Theory Comput; 2015 Jun; 11(6):2827-40. PubMed ID: 26575575
[TBL] [Abstract][Full Text] [Related]
60. Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.
Emperador A; Meyer T; Orozco M
Proteins; 2010 Jan; 78(1):83-94. PubMed ID: 19816993
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]