Molecular Modeling of Proteins

by Andreas Kukol (Editor)

Overview

Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins, and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions, and notes on troubleshooting and avoiding common pitfalls.

Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical, and biosciences interested in utilizing this powerful technology.

Product Details

ISBN-13:	9781493914647
Publisher:	Springer New York
Publication date:	10/21/2014
Series:	Methods in Molecular Biology , #1215
Edition description:	2nd ed. 2015
Pages:	474
Product dimensions:	6.90(w) x 10.10(h) x 1.30(d)

Table of Contents

Preface     v
Contributors     ix
Methodology
Molecular Dynamics Simulations   Erik R. Lindahl     3
Monte Carlo Simulations   David J. Earl   Michael W. Deem     25
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
Comparison of Protein Force Fields for Molecular Dynamics Simulations   Olgun Guvench   Alexander D. MacKerell, Jr.     63
Normal Modes and Essential Dynamics   Steven Hayward   Bert L. de Groot     89
Free Energy Calculations
Calculation of Absolute Protein-Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method   Hyung-June Woo     109
Free Energy Calculations Applied to Membrane Proteins   Christophe Chipot     121
Molecular Modeling of Membrane Proteins
Molecular Dynamics Simulations of Membrane Proteins   Philip C. Biggin   Peter J. Bond     147
Membrane-Associated Proteins and Peptides   Marc F. Lensink     161
Implicit Membrane Models for Membrane Protein Simulation   Michael Feig     181
Protein Structure Determination
Comparative Modeling of Proteins   Gerald H. Lushington     199
Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints   Andrew J. Beevers   Andreas Kukol     213
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
Conformational Change
Conformational Changes in Protein Function   Haiguang Liu   Shubhra Ghosh Dastidar   Hongxing Lei   Wei Zhang   Matthew C. Lee   Yong Duan     259
Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations   Hongxing Lei   Yong Duan     277
Modeling of Protein Misfolding in Disease   Edyta B. Malolepsza     297
Applications to Drug Design
Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking   David S. Wishart     333
Receptor Flexibility for Large-Scale In Silico Ligand Screens: Chances and Challenges   B. Fischer   H. Merlitz   W. Wenzel     353
Molecular Docking   Garrett M. Morris   Marguerita Lim-Wilby     365
Index     383

Editorial Reviews

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)

From the Publisher