Molecular Modeling of Proteins Book

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 Modeling of Proteins 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