Molecular Modeling of Proteins
Molecular modeling has undergone a remarkable transformation in the last 20 years. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists - especially those new to the software...
Molecular modeling has undergone a remarkable transformation in the last 20 years. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists - especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.
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 IdentifyingPutative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking - David S. Wishart
18 Receptor flexibility for large scale
19 Molecular docking - Garrett M. Morris and Marguerita Lim-Wilby
- 2008, 390 Seiten, Maße: 16,3 x 24,4 cm, Gebunden, Englisch
- Herausgegeben: Andreas Kukol
- Verlag: Humana Press
- ISBN-10: 1588298647
- ISBN-13: 9781588298645
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