[gmx-users] Re: combining differently-generated force-fields

[Kukol, Andreas]

This book is out now:

Molecular Modeling of Proteins

# Hardcover: 396 pages
# Publisher: Humana Press; 1 edition (February 19, 2008)
# Language: English
# ISBN-10: 1588298647
# ISBN-13: 978-1588298645

Here is a list of contents:

Methodology
1 Molecular dynamics simulations
Erik R. Lindahl

2 Monte Carlo simulations
Michael W. Deem, David J. Earl

3 Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes
Jiali Gao, Dan. T. Major, Yao Fan, Yen-lin Lin, Shuhua Ma and Kin-Yiu Wong

4 Comparison of forcefields for molecular dynamics simulations
Olgun Guvench and Alexander D. MacKerell, Jr.

5 Normal modes and essential dynamics
Steven Hayward and Bert L. de Groot

Free energy calculations
6 Calculation of absolute protein-ligand binding constants with the molelcular dynamics free energy perturbation method
Hyung-June Woo

7 Free energy calculations applied to membrane proteins
Christophe Chipot

Molecular modeling of membrane proteins
8 Molecular dynamics simulations of membrane proteins
Philip C. Biggin and Peter J. Bond

9 Membrane associated proteins and peptides
Mark F. Lensink

10 Implicit membrane models for membrane protein simulation
Michael Feig

Protein structure determination

11 Comparative protein modeling
Gerald H. Lushington

12 Transmembrane protein models based on high throughput MD simulations with experimental constraints
Andrew J. Beevers, Andreas Kukol

13 NMR-based modelling and refinement of protein 3D structures and their complexes
G Fuentes, A.D.J. van Dijk and Alexandre M.J.J. Bonvin

Conformational change
14 Conformational changes in protein function
Haiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, and Yong Duan

15 Protein folding and unfolding by all-atom molecular dynamics simulations
Hongxing Lei and Yong Duan

16 Modeling of protein misfolding in disease
Edyta B. Malolepsza

Applications to drug design
17 Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking
David S. Wishart

18 Receptor flexibility for large scale in-silico ligand screens: chances and challenges
B. Fisher, H. Merlitz and Wolfgang Wenzel

19 Molecular docking
Garrett M. Morris and Marguerita Lim-Wilby

Best wishes
Andreas

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of chris.neale at utoronto.ca
> Sent: 03 May 2008 15:58
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: combining differently-generated force-fields
>
> Thanks Soo Mei, that might be interesting. I couldn't access it
> either. I think it is a book (http://www.springer.com/series/7651)
>
> MacKerell's website indicates that it is not yet in press, although I
> am not sure how recently that was updated:
>
> Guvench, O. and MacKerell, A.D., Jr., ?Comparison of protein force
> fields for molecular dynamics simulations,? In Molecular Modeling of
> Proteins, A. Kukol,
> Editor, Humana Press, Submitted.
>
> --original message --
>
> A related reference might be this?
>
> Comparison of protein force fields for molecular dynamics simulations.
>       Methods Mol Biol. 2008;443:63-88.
> Guvench O, Mackerell AD Jr.
>
> Not that I've read it yet, because my institute doesn't have access to
> that journal.
>
> Cheers,
> Soo Mei
>
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