Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

Dynamics Simulation ◽

Implicit Solvent ◽

Energy Landscapes ◽

Small Peptides ◽

Implicit Solvent Model ◽

Solvent Model ◽

Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes”

10.1021/acs.jpcb.8b04187 ◽

2018 ◽

Vol 124 (6) ◽

pp. 1115-1123

Author(s):

Vytautas Gapsys ◽

Morteza Khabiri ◽

Bert L. de Groot ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Analysis of the Free Energy Landscapes for the Opening–Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation

10.1021/acs.jpcb.5b05432 ◽

2015 ◽

Vol 119 (30) ◽

pp. 9717-9725 ◽

Cited By ~ 8

Author(s):

Wei-Lin Hsu ◽

Tadaomi Furuta ◽

Minoru Sakurai

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Enhanced Sampling ◽

Maltose Transporter ◽

1P587 Folding free-energy landscapes of 10-residue proteins(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s293_3 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S293

Author(s):

Daisuke Satoh ◽

Kentaro Shimizu ◽

Shugo Nakamura ◽

Tohru Terada

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Poster Session ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Meeting Program ◽

Free Energy Landscapes ◽

Folding Free Energy

Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein–DNA Binding Free Energy Landscapes

10.1021/acs.jpcb.6b12450 ◽

2017 ◽

Vol 121 (20) ◽

pp. 5151-5161 ◽

Cited By ~ 11

Author(s):

Morteza Khabiri ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Correction to “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein–DNA Binding Free Energy Landscapes”

10.1021/acs.jpcb.0c10359 ◽

2020 ◽

Vol 124 (49) ◽

pp. 11311-11311

Author(s):

Morteza Khabiri ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20104 ◽

2004 ◽

Vol 56 (2) ◽

pp. 310-321 ◽

Cited By ~ 97

Author(s):

Anthony K. Felts ◽

Yuichi Harano ◽

Emilio Gallicchio ◽

Ronald M. Levy

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Implicit Solvent ◽

Helical Peptides ◽

Replica Exchange Molecular Dynamics ◽

Implicit Solvent Model ◽

Solvent Model ◽

Energy Surfaces

Molecular Dynamics Calculation of Interaction Forces between Colloids in Aqueous Electrolyte Solutions Using an Implicit Solvent Model

KAGAKU KOGAKU RONBUNSHU ◽

10.1252/kakoronbunshu.31.295 ◽

2005 ◽

Vol 31 (5) ◽

pp. 295-300 ◽

Cited By ~ 1

Author(s):

Shintaro Morisada ◽

Kenji Muranishi ◽

Hiroyuki Shinto ◽

Ko Higashitani

Keyword(s):

Molecular Dynamics ◽

Aqueous Electrolyte ◽

Electrolyte Solutions ◽

Implicit Solvent ◽

Interaction Forces ◽

Implicit Solvent Model ◽

Aqueous Electrolyte Solutions ◽

Solvent Model ◽

Dynamics Calculation

Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽

10.3390/biology1020245 ◽

2012 ◽

Vol 1 (2) ◽

pp. 245-259

Author(s):

Yoshifumi Fukunishi ◽

Saki Hongo ◽

Masami Lintuluoto ◽

Hiroshi Matsuo

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dynamics Simulation ◽

Energy Profile ◽

Free Energy Profile

3D-QSAR, docking, molecular dynamics simulation and free energy calculation studies of some pyrimidine derivatives as novel JAK3 inhibitors

Arabian Journal of Chemistry ◽

10.1016/j.arabjc.2017.09.009 ◽

2020 ◽

Vol 13 (1) ◽

pp. 1052-1078 ◽

Cited By ~ 9

Author(s):

Anand Balupuri ◽

Pavithra K. Balasubramanian ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Pyrimidine Derivatives

Free energy and scalings for polymer translocation through a nanopore: A molecular dynamics simulation study combined with milestoning

Physics Letters A ◽

10.1016/j.physleta.2011.12.014 ◽

2012 ◽

Vol 376 (4) ◽

pp. 290-292 ◽

Cited By ~ 3

Author(s):

Xiang-Gui Xue ◽

Li Zhao ◽

Zhong-Yuan Lu ◽

Ze-Sheng Li

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Simulation Study ◽

Dynamics Simulation ◽

Polymer Translocation