Subject: free energy summary

From: Pierre Mignon <[email-masked]>
Date: Wed, 29 May 2002 11:17:53 +0200 (MEST)

Hello, here are the answers I got from my question upon free energy calculation. Thank's for the informations.

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The following references will provide the information about free energy 
calculation in bio-molecules. 

1) M. Rami Reddy, Mark Erion, and Atul Agarwal' Free Energy Calculations: 
Use and Limitations in Predicting Ligand Binding Affinities' Reviews in 
Computational Chemistry, Edited by Lipkowitz and Boyd, Volume 16, Pages 
217-303. 

2) Free Energy Calculations in Rational Drug Design (a total of 19 chapters 
in this text book and all are related to free energy calculations), edited 
by M. Rami Reddy and Mark Erion, Kluwer Academic/Plenum Publishers, New 
York, 2001. 

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Dear Pierre, 

here is a little bit longish list of articles from my collection. 

About the more rigorous methods: 

@article{70807, 
author = {P. Kollman}, 
title = {Free Energy Calculations: Applications to Chemical and 
Biochemical Phenomena}, 
journal = {Chem.Rev.}, 
volume = {93}, 
pages = {2395-2417}, 
year = {1993}, 
keywords = {Review ; AMBER ; free energy ; binding energy ; molecular 
dynamics ; molecular modelling} 
} 

@article{70809, 
author = {D. L. Beveridge and F. M. DiCapua}, 
title = {Free energy via molecular simulation: application to 
chemical and biomolecular systems}, 
journal = {Annu.Rev.Biophys.Biophys.Chem.}, 
volume = {18}, 
pages = {431-492}, 
year = {1989}, 
keywords = {free energy ; Review ; molecuar dynamics ; fundamentals} 
} 

@article{70820, 
author = {M. Mezei and D. L. Beveridge}, 
title = {Free Energy Simulations}, 
journal = {Ann.NY Acad.Sci.}, 
volume = {482}, 
pages = {1-23}, 
year = {1986}, 
keywords = {free energy ; Review ; molecular dynamics ; ligand 
docking} 
} 

@incollection{80101, 
author = {A. E. Mark and W. F. van Gunsteren}, 
editor = {P. M. Dean and G. Jolles and C. G. Newton}, 
title = {Free Energy Calculations in Drug Design: A Practical Guide}, 
booktitle = {New Perspectives in Drug Design}, 
chapter = {10}, 
pages = {185-200}, 
publisher = {Academic Press}, 
year = {1995}, 
keywords = {drug design ; binding energy ; molecular dynamics ; 
gromos} 
} 

@article{80122, 
author = {J. A. McCammon}, 
title = {Free energy from simulation}, 
journal = {Curr.Op.Struct.Biol.}, 
volume = {1}, 
pages = {196-200}, 
year = {1991}, 
keywords = {free energy ; ligand docking ; free energy calculation} 
} 

About the MM-PBSA which is less rigorous but faster: 

@article{80023, 
author = {J. Wang and P. Morin and W. Wang and P. Kollman}, 
title = {Use of MM-PBSA in reproducing the binding free energies to 
HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT 
of efavirenz by docking and MM-PBSA}, 
journal = {J.Am.Chem.Soc.}, 
volume = {123}, 
pages = {5221-5230}, 
year = {2001}, 
keywords = {free energy ; ligand docking ; molecular dynamics ; AMBER 
; MM-PBSA} 
} 

@article{70831, 
author = {W. Wang and O. Donini and C. M. Reyes and P. A. Kollman}, 
title = {Biomolecular simulations: recent developments in force 
fields, simulations of enzyme catalysis, protein--ligand, 
protein--protein, and protein-nucleic acid noncovalent interactions}, 
journal = {Ann.Rev.Biophys.Biomol.Struct.}, 
volume = {30}, 
pages = {211-243}, 
year = {2001}, 
keywords = {force field ; Review ; drug design ; ligand docking ; 
protein protein interactions ; protein nucleic acid interaction ; 
protein rna interactions ; protein dna interactions} 
} 

A very general review focused on calculation of binding energies (very 
good introduction): 

@article{80029, 
author = {M. L. Lamb and W. L. Jorgensen}, 
title = {Computational approaches to molecular recognition}, 
journal = {Curr.Op.Chem.Biol.}, 
volume = {1}, 
pages = {449-457}, 
year = {1997}, 
keywords = {recognition} 
} 

Hope this helps, 

Oliver. 

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This is shamefully self-promoting, but the excellent 
recent book "Computational Biochemistry & Biophysics" 
(eds. Becker, Mackerell, Roux, Watanabe; Marcel Dekker) 
has a free energy overview chapter by yours truly... 

Tom Simonson 

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Dear Pierre : 

At 

http://www.biophysics.org/img/Bloomfield.V-Thermo.pdf 

you will find an excellent review on Thermodynamics and Statistical Thermodynamics. There is a lot of information on free energy in biological system. As a favor please sumarize this discussion or send me the results, because I am also working on 
it. 

Best 

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Mignon Pierre
PhD student
Free University of Brussel (VUB)         
Dienst Algemene Chemie (ALGC)               
Pleinlaan, 2                            
1050 Brussels
Belgium
Tel + 32 2 629 35 16                                 
Fax + 32 2 629 33 17
e-mail [email-masked]