free energy summary

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:
  at.at 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}
 }
  at.at 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}
 }
  at.at 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}
 }
  at.at 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}
 }
  at.at 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:
  at.at 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}
 }
  at.at 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):
  at.at 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.
 ******************************************************************************
 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
 ******************************************************************************
 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 pmignon at.at vub.ac.be