Literature DB >> 3504214

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry.

W F van Gunsteren1, H J Berendsen.   

Abstract

A new and promising development in the field of computer simulation of molecular systems is the so-called thermodynamic cycle integration technique, which combines well-known results from statistical thermodynamics with powerful computer simulation methods. The basic formulas, the development and the applications in the areas of drug design, protein engineering and conformational analysis of this elegant technique are discussed.

Mesh:

Year:  1987        PMID: 3504214     DOI: 10.1007/BF01676960

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  4 in total

1.  Theoretical calculation of relative binding affinity in host-guest systems.

Authors:  T P Lybrand; J A McCammon; G Wipff
Journal:  Proc Natl Acad Sci U S A       Date:  1986-02       Impact factor: 11.205

2.  Free energy simulations.

Authors:  M Mezei; D L Beveridge
Journal:  Ann N Y Acad Sci       Date:  1986       Impact factor: 5.691

3.  Molecular dynamics: perspective for complex systems.

Authors:  W F Van Gunsteren; H J Berendsen
Journal:  Biochem Soc Trans       Date:  1982-10       Impact factor: 5.407

4.  Calculation of the relative change in binding free energy of a protein-inhibitor complex.

Authors:  P A Bash; U C Singh; F K Brown; R Langridge; P A Kollman
Journal:  Science       Date:  1987-01-30       Impact factor: 47.728

  4 in total
  15 in total

Review 1.  Molecular recognition: models for drug design.

Authors:  R J Breckenridge
Journal:  Experientia       Date:  1991-12-01

2.  A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase.

Authors:  N R Taylor; M von Itzstein
Journal:  J Comput Aided Mol Des       Date:  1996-06       Impact factor: 3.686

3.  Molecular dynamics study of peptide-bilayer adsorption.

Authors:  C M Shepherd; K A Schaus; H J Vogel; A H Juffer
Journal:  Biophys J       Date:  2001-02       Impact factor: 4.033

4.  Dynamic simulation as an essential tool in molecular modeling.

Authors:  H J Berendsen
Journal:  J Comput Aided Mol Des       Date:  1988-10       Impact factor: 3.686

5.  Polarizable water model for the coarse-grained MARTINI force field.

Authors:  Semen O Yesylevskyy; Lars V Schäfer; Durba Sengupta; Siewert J Marrink
Journal:  PLoS Comput Biol       Date:  2010-06-10       Impact factor: 4.475

6.  Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains.

Authors:  Wei Han; Klaus Schulten
Journal:  J Chem Theory Comput       Date:  2012-10-11       Impact factor: 6.006

7.  An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency.

Authors:  Yanzi Zhou; Syed M Moin; Sinisa Urban; Yingkai Zhang
Journal:  Structure       Date:  2012-06-14       Impact factor: 5.006

8.  Drug design for ever, from hype to hope.

Authors:  G Seddon; V Lounnas; R McGuire; T van den Bergh; R P Bywater; L Oliveira; G Vriend
Journal:  J Comput Aided Mol Des       Date:  2012-01-18       Impact factor: 3.686

9.  The future of molecular dynamics simulations in drug discovery.

Authors:  David W Borhani; David E Shaw
Journal:  J Comput Aided Mol Des       Date:  2011-12-20       Impact factor: 3.686

10.  Binding affinities controlled by shifting conformational equilibria: opportunities and limitations.

Authors:  Servaas Michielssens; Bert L de Groot; Helmut Grubmüller
Journal:  Biophys J       Date:  2015-05-19       Impact factor: 4.033

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