Molecular modeling of proteins / Andreas Kukol [editor].

Format:

Book

Contributor:

Kukol, Andreas.

Series:

Methods in molecular biology (Clifton, N.J.) ; 443.

Methods in molecular biology, 1064-3745 ; 443

Language:

English

Subjects (All):

Proteins.

Biological models.

Computer simulation.

Models, Molecular.

Computer Simulation.

Medical Subjects:

Proteins.

Models, Molecular.

Computer Simulation.

Physical Description:

xi, 390 pages : illustrations ; 25 cm.

Place of Publication:

Totowa, NJ : Humana Press, [2008]

Summary:

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 nonspecialists-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, from free energy calculation to applications for drug design. Written by a panel of internationally distinguished 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.

Contents:

Part I Methodology

1 Molecular Dynamics Simulations / Erik R. Lindahl 3

2 Monte Carlo Simulations / David J. Earl, Michael W. Deem 25

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, Kin-Yiu Wong 37

4 Comparison of Protein Force Fields for Molecular Dynamics Simulations / Olgun Guvench, Alexander D. MacKerell, Jr. 63

5 Normal Modes and Essential Dynamics / Steven Hayward, Bert L. de Groot 89

Part II Free Energy Calculations

6 Calculation of Absolute Protein-Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method / Hyung-June Woo 109

7 Free Energy Calculations Applied to Membrane Proteins / Christophe Chipot 121

Part III Molecular Modeling of Membrane Proteins

8 Molecular Dynamics Simulations of Membrane Proteins / Philip C. Biggin, Peter J. Bond 147

9 Membrane-Associated Proteins and Peptides / Marc F. Lensink 161

10 Implicit Membrane Models for Membrane Protein Simulation / Michael Feig 181

Part IV Protein Structure Determination

11 Comparative Modeling of Proteins / Gerald H. Lushington 199

12 Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints / Andrew J. Beevers, Andreas Kukol 213

13 Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes / Gloria Fuentes, Aalt D.J. van Dijk, Alexandre M.J.J. Bonvin 229

Part V Conformational Change

14 Conformational Changes in Protein Function / Haiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, Yong Duan 259

15 Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations / Hongxing Lei, Yong Duan 277

16 Modeling of Protein Misfolding in Disease / Edyta B. Malolepsza 297

Part VI Applications to Drug Design

17 Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking / David S. Wishart 333

18 Receptor Flexibility for Large-Scale In Silico Ligand Screens: Chances and Challenges / B. Fischer, H. Merlitz, W. Wenzel 353

19 Molecular Docking / Garrett M. Morris, Marguerita Lim-Wilby 365.

Notes:

Includes bibliographical references and index.

ISBN:

9781588298645

1588298647

OCLC:

172979419