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Molecular Modeling of Proteins

Edited by A Kukol 
Humana Press  May 2008  



Hardcover  390 pp  ISBN 9781588298645      £81.00
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.

Written for chemists, biochemists, biologists, biophysicists, bioinformatics scientists

Contents

Preface
Contributors

Part I Methodology

  • Molecular Dynamics Simulations - Erik R. Lindahl
  • Monte Carlo Simulations - David J. Earl and Michael W. Deem
  • 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
  • Comparison of Protein Force Fields for Molecular Dynamics Simulations - Olgun Guvench and Alexander D. MacKerell, Jr.
  • Normal Modes and Essential Dynamics - Steven Hayward and Bert L. de Groot

Part II Free Energy Calculations

  • Calculation of Absolute Protein-Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method - Hyung-June Woo
  • Free Energy Calculations Applied to Membrane Proteins - Christophe Chipot

Part III Molecular Modeling of Membrane Proteins

  • Molecular Dynamics Simulations of Membrane Proteins - Philip C. Biggin and Peter J. Bond
  • Membrane-Associated Proteins and Peptides - Marc F. Lensink
  • Implicit Membrane Models for Membrane Protein Simulation - Michael Feig

Part IV Protein Structure Determination

  • Comparative Modeling of Proteins - Gerald H. Lushington
  • Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints - Andrew J. Beevers and Andreas Kukol
  • Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes - Gloria Fuentes, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin

Part V Conformational Change

  • Conformational Changes in Protein Function - Haiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, and Yong Duan
  • Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations - Hongxing Lei and Yong Duan
  • Modeling of Protein Misfolding in Disease - Edyta B. Ma?olepsza

Part VI Applications to Drug Design

  • Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking - David S. Wishart
  • Receptor Flexibility for Large-Scale In Silico Ligand Screens: Chances and Challenges - B. Fischer, H. Merlitz, and W. Wenzel
  • Molecular Docking - Garrett M. Morris and Marguerita Lim-Wilby Index

    To find similar publications, click on a keyword below:
    Springer : biochemistry : biotechnology : modelling, computer & mathematical : molecular biology : proteins

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