Treatment of rotational isomers in free energy calculations. II. Molecular dynamics simulation study of 18‐crown‐6 in aqueous solution as an example of systems with large numbers of rotational isomeric states

Simulation Study ◽

Dynamics Simulation ◽

Energy Calculations ◽

Rotational Isomers ◽

Large Numbers

Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study

Molecular Physics ◽

10.1080/00268979400100344 ◽

1994 ◽

Vol 82 (3) ◽

pp. 455-471 ◽

Cited By ~ 51

Author(s):

Alexander P. Lyubartsev ◽

Aatto Laaksonen ◽

Pavel N. Vorontsov-Velyaminov

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Free Energy ◽

Simulation Study ◽

Dynamics Simulation ◽

Energy Calculations ◽

Lennard Jones ◽

Expanded Ensemble

Molecular Dynamics Simulation Study on CO2 Physical Absorption Mechanisms for Ethylene-Glycol-Based Solvents Using Free Energy Calculations

Industrial & Engineering Chemistry Research ◽

10.1021/acs.iecr.6b01074 ◽

2016 ◽

Vol 55 (29) ◽

pp. 8200-8206 ◽

Cited By ~ 4

Author(s):

Ryo Nagumo ◽

Yukihiro Muraki ◽

Shuichi Iwata ◽

Hideki Mori ◽

Hiromitsu Takaba ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ethylene Glycol ◽

Simulation Study ◽

Dynamics Simulation ◽

Energy Calculations ◽

Physical Absorption

Refinement of X-ray data on dual cosubstrate specificity of CK2 kinase by free energy calculations based on molecular dynamics simulation

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20350 ◽

2004 ◽

Vol 58 (3) ◽

pp. 511-517 ◽

Cited By ~ 6

Author(s):

Piotr Setny ◽

Maciej Geller

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dynamics Simulation ◽

Energy Calculations ◽

X Ray ◽

Ck2 Kinase

The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-010-9408-7 ◽

2011 ◽

Vol 25 (2) ◽

pp. 171-180 ◽

Cited By ~ 18

Author(s):

Yuanhua Cheng ◽

Wei Cui ◽

Quan Chen ◽

Chen-Ho Tung ◽

Mingjuan Ji ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Mechanism ◽

Aurora Kinase ◽

Dynamics Simulation ◽

Aurora Kinase A ◽

Energy Calculations ◽

Kinase A

Molecular dynamics simulation and free energy calculations of symmetric fluoro-substituted diol-based HIV-1 protease inhibitors

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2008.11.029 ◽

2009 ◽

Vol 899 (1-3) ◽

pp. 1-8 ◽

Cited By ~ 4

Author(s):

Jian-Zhong Chen ◽

Mao-You Yang ◽

Chang-Hong Yi ◽

Shu-Hua Shi ◽

Qing-Gang Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Protease Inhibitors ◽

Dynamics Simulation ◽

Energy Calculations ◽

Hiv 1

Effects of single-walled carbon nanotube on the conformation of human hepcidin: molecular dynamics simulation and binding free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1477624 ◽

2018 ◽

Vol 37 (8) ◽

pp. 2125-2132 ◽

Cited By ~ 3

Author(s):

Reza Rasoolzadeh ◽

Faramarz Mehrnejad ◽

Majid Taghdir ◽

Parichehreh Yaghmaei

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Carbon Nanotube ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Single Walled Carbon Nanotube ◽

Energy Calculations ◽

Binding Free Energy Calculations

Some practical aspects of free energy calculations from molecular dynamics simulation

Journal of Computational Chemistry ◽

10.1002/(sici)1096-987x(199906)20:8<877::aid-jcc12>3.0.co;2-o ◽

1999 ◽

Vol 20 (8) ◽

pp. 877-885 ◽

Cited By ~ 1

Author(s):

Srikanta Sen ◽

Lennart Nilsson

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dynamics Simulation ◽

Energy Calculations

Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2016.1160259 ◽

2016 ◽

Vol 35 (4) ◽

pp. 755-764 ◽

Cited By ~ 4

Author(s):

Dong-Ru Sun ◽

Qing-Chuan Zheng ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Small Molecule ◽

Small Molecule Inhibitors ◽

Interaction Mechanism ◽

Dynamics Simulation ◽

Energy Calculations

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Journal of Molecular Modeling ◽

10.1007/s00894-013-1997-3 ◽

2013 ◽

Vol 19 (11) ◽

pp. 5097-5112 ◽

Cited By ~ 5

Author(s):

Shi-Feng Chen ◽

Yang Cao ◽

Jiong-Jiong Chen ◽

Jian-Zhong Chen

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dynamics Simulation ◽

Binding Selectivity ◽

Energy Calculations ◽

Selectivity Studies

Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors

BMC Systems Biology ◽

10.1186/s12918-017-0385-5 ◽

2017 ◽

Vol 11 (S2) ◽

Cited By ~ 6

Author(s):

Pavithra K. Balasubramanian ◽

Anand Balupuri ◽

Hee-Young Kang ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Kinase Inhibitors ◽

3D Qsar ◽

Dynamics Simulation ◽

Energy Calculations ◽

Qsar Studies