Cumulant expansion of the free energy: Application to free energy derivatives and component analysis

G. Archontis; M. Karplus

doi:10.1063/1.472921

Cumulant expansion of the free energy: Application to free energy derivatives and component analysis

The Journal of Chemical Physics ◽

10.1063/1.472921 ◽

1996 ◽

Vol 105 (24) ◽

pp. 11246-11260 ◽

Cited By ~ 20

Author(s):

G. Archontis ◽

M. Karplus

Keyword(s):

Free Energy ◽

Component Analysis ◽

Cumulant Expansion ◽

Energy Derivatives ◽

Energy Application

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Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21185 ◽

2006 ◽

Vol 65 (4) ◽

pp. 898-913 ◽

Cited By ~ 23

Author(s):

Phuong H. Nguyen

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Principal Component ◽

Component Analysis ◽

Energy Landscapes ◽

Nonlinear Principal Component Analysis ◽

Free Energy Landscapes

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Free-energy component analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level

Journal of Computational Chemistry ◽

10.1002/jcc.10009 ◽

2001 ◽

Vol 23 (1) ◽

pp. 1-14 ◽

Cited By ~ 69

Author(s):

B. Jayaram ◽

K. McConnell ◽

S. B. Dixit ◽

A. Das ◽

D. L. Beveridge

Keyword(s):

Free Energy ◽

Molecular Level ◽

Component Analysis ◽

Dna Complexes ◽

Energy Component ◽

Consensus View

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Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease−Inhibitor Binding

Journal of Medicinal Chemistry ◽

10.1021/jm010175z ◽

2001 ◽

Vol 44 (25) ◽

pp. 4325-4338 ◽

Cited By ~ 26

Author(s):

Parul Kalra ◽

T. Vasisht Reddy ◽

B. Jayaram

Keyword(s):

Free Energy ◽

Drug Design ◽

Protease Inhibitor ◽

Component Analysis ◽

Inhibitor Binding ◽

Energy Component ◽

Hiv 1

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Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

The Journal of Physical Chemistry Letters ◽

10.1021/jz101069e ◽

2010 ◽

Vol 1 (19) ◽

pp. 2769-2773 ◽

Cited By ~ 20

Author(s):

Abhinav Jain ◽

Rainer Hegger ◽

Gerhard Stock

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Principal Component ◽

Component Analysis ◽

Energy Landscapes ◽

Free Energy Landscapes

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The cumulant expansion of the free energy of disordered systems and the spin glass transition

Physics Letters A ◽

10.1016/0375-9601(80)90751-3 ◽

1980 ◽

Vol 76 (5-6) ◽

pp. 421-423 ◽

Cited By ~ 3

Author(s):

S. Goulart Rosa

Keyword(s):

Free Energy ◽

Glass Transition ◽

Spin Glass ◽

Disordered Systems ◽

Cumulant Expansion ◽

Spin Glass Transition

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Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis

The Journal of Physical Chemistry B ◽

10.1021/jp9076036 ◽

2009 ◽

Vol 113 (52) ◽

pp. 16660-16668 ◽

Cited By ~ 36

Author(s):

Laura Riccardi ◽

Phuong H. Nguyen ◽

Gerhard Stock

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Dihedral Angle ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Free Energy Landscape ◽

Rna Hairpins

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Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2019.07.008 ◽

2019 ◽

Vol 92 ◽

pp. 112-122 ◽

Cited By ~ 3

Author(s):

Konda Reddy Karnati ◽

Yixuan Wang

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Principal Component ◽

Component Analysis ◽

Ligand Interactions ◽

Dynamics Simulations ◽

Hiv 1

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Free-energy derivatives and structure optimization within quasiharmonic lattice dynamics

Physical Review B ◽

10.1103/physrevb.56.14380 ◽

1997 ◽

Vol 56 (22) ◽

pp. 14380-14390 ◽

Cited By ~ 70

Author(s):

M. B. Taylor ◽

G. D. Barrera ◽

N. L. Allan ◽

T. H. K. Barron

Keyword(s):

Free Energy ◽

Lattice Dynamics ◽

Structure Optimization ◽

Energy Derivatives

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Free energy derivatives: A new method for probing the convergence problem in free energy calculations

Journal of Computational Chemistry ◽

10.1002/jcc.540150112 ◽

1994 ◽

Vol 15 (1) ◽

pp. 105-123 ◽

Cited By ~ 42

Author(s):

David A. Pearlman

Keyword(s):

Free Energy ◽

Free Energy Calculations ◽

New Method ◽

Convergence Problem ◽

Energy Calculations ◽

Energy Derivatives

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Correlation of the kinetics of electron-transfer processes with the change in reaction free energy. Application to electron-exchanged-initiated chemiluminescence reactions

Journal of the American Chemical Society ◽

10.1021/ja00513a077 ◽

1979 ◽

Vol 101 (19) ◽

pp. 5851-5853 ◽

Cited By ~ 27

Author(s):

Gary B. Schuster

Keyword(s):

Electron Transfer ◽

Free Energy ◽

Transfer Processes ◽

Reaction Free Energy ◽

Energy Application ◽

Electron Transfer Processes ◽

Kinetics Of

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