Molecular Modeling of Proteins

ISBN-13: 9781588298645 / Angielski / Twarda / 2008 / 390 str.

Andreas Kukol

Opis

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."

Recenzje

From the reviews:

"This book covers many different aspects of protein modeling and is just one volume in an extremely large series ... . might be useful as an overview of the various techniques and methods used for the molecular modeling of proteins." (Andrzej Kloczkowski and Robert L. Jernigan, Journal of the American Chemical Society, Vol. 130 (37), 2008)

Spis treści

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 IdentifyingPutative 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

O autorze

Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. 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, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, the book is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics. Links to downloadable software made available by the authors are also provided.

Blurb

Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. Molecular Modeling of Proteins 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 this book, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, Molecular Modeling of Proteins is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics.