Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations

Guodong Hu; Shicai Xu; Jihua Wang

doi:10.1111/cbdd.12598

Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations

Chemical Biology & Drug Design ◽

10.1111/cbdd.12598 ◽

2015 ◽

Vol 86 (6) ◽

pp. 1351-1359 ◽

Cited By ~ 15

Author(s):

Guodong Hu ◽

Shicai Xu ◽

Jihua Wang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Steered Molecular Dynamics ◽

Free Energy Landscape ◽

Mdm2 Protein ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Dynamics Simulations

Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations

Biophysical Chemistry ◽

10.1016/j.bpc.2010.05.014 ◽

2010 ◽

Vol 151 (3) ◽

pp. 178-180 ◽

Cited By ~ 7

Author(s):

L.Y. Chen

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Steered Molecular Dynamics ◽

Free Energy Landscape ◽

Dynamics Simulations

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0608432104 ◽

2007 ◽

Vol 104 (12) ◽

pp. 4925-4930 ◽

Cited By ~ 176

Author(s):

H. Lei ◽

C. Wu ◽

H. Liu ◽

Y. Duan

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Free Energy Landscape ◽

Villin Headpiece ◽

Dynamics Simulations ◽

Folding Free Energy

Molecular Recognition in a Diverse Set of Protein–Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations

Journal of Chemical Information and Modeling ◽

10.1021/ci400312v ◽

2013 ◽

Vol 53 (10) ◽

pp. 2659-2670 ◽

Cited By ~ 26

Author(s):

Bo Wang ◽

Liwei Li ◽

Thomas D. Hurley ◽

Samy O. Meroueh

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Recognition ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Energy Calculations ◽

End Point ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Dynamics Simulations

A manifestation of the Ostwald step rule: Molecular-dynamics simulations and free-energy landscape of the primary nucleation and melting of single-molecule polyethylene in dilute solution

The Journal of Chemical Physics ◽

10.1063/1.2102889 ◽

2005 ◽

Vol 123 (14) ◽

pp. 144907 ◽

Cited By ~ 18

Author(s):

L. Larini ◽

D. Leporini

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Energy Landscape ◽

Free Energy Landscape ◽

Dilute Solution ◽

Primary Nucleation ◽

Ostwald Step Rule ◽

Dynamics Simulations

Author response: Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

10.7554/elife.22175.024 ◽

2017 ◽

Cited By ~ 1

Author(s):

Antonija Kuzmanic ◽

Ludovico Sutto ◽

Giorgio Saladino ◽

Angel R Nebreda ◽

Francesco L Gervasio ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Map Kinase ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Author Response ◽

Free Energy Landscape ◽

Dynamics Simulations ◽

P38α Map Kinase

Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct200911w ◽

2012 ◽

Vol 8 (4) ◽

pp. 1471-1479 ◽

Cited By ~ 28

Author(s):

Laura Riccardi ◽

Phuong H. Nguyen ◽

Gerhard Stock

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Free Energy Landscape ◽

Peptide Aggregation ◽

Dynamics Simulations

Recent Advances in Protein−Ligand Interactions: Molecular Dynamics Simulations and Binding Free Energy

Current Computer - Aided Drug Design ◽

10.2174/15734099113096660036 ◽

2013 ◽

Vol 9 (4) ◽

pp. 518-531 ◽

Cited By ~ 17

Author(s):

Kshatresh Dubey ◽

Rakesh Tiwari ◽

Rajendra Ojha

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Protein Ligand Interactions ◽

Recent Advances ◽

Ligand Interactions ◽

Dynamics Simulations

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2009.01.006 ◽

2009 ◽

Vol 27 (8) ◽

pp. 889-899 ◽

Cited By ~ 114

Author(s):

Elena Papaleo ◽

Paolo Mereghetti ◽

Piercarlo Fantucci ◽

Rita Grandori ◽

Luca De Gioia

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Free Energy Landscape ◽

Structural Clustering ◽

Dynamics Simulations

Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

PLoS ONE ◽

10.1371/journal.pone.0101951 ◽

2014 ◽

Vol 9 (7) ◽

pp. e101951 ◽

Cited By ~ 13

Author(s):

Hisashi Ishida ◽

Atsushi Matsumoto

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Free Energy Landscape ◽

Density Maps ◽

Trna Translocation ◽

Dynamics Simulations

Free energy landscape of electrocatalytic CO 2 reduction to CO on aqueous FeN 4 center embedded graphene studied by ab initio molecular dynamics simulations

Chemical Physics Letters ◽

10.1016/j.cplett.2017.09.052 ◽

2017 ◽

Vol 688 ◽

pp. 37-42 ◽

Cited By ~ 6

Author(s):

Tian Sheng ◽

Shi-Gang Sun

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Ab Initio Molecular Dynamics ◽

Free Energy Landscape ◽

Dynamics Simulations