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Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions - 1st Edition - ISBN: 9780128020036, 9780128020180

Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions, Volume 100

1st Edition

Serial Volume Editor: Tatyana Karabencheva-Christova
Hardcover ISBN: 9780128020036
eBook ISBN: 9780128020180
Imprint: Academic Press
Published Date: 24th September 2015
Page Count: 330
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Table of Contents

  • Preface
  • Acknowledgments
  • Chapter One: PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems
    • Abstract
    • 1 Introduction
    • 2 QM/MM-MD Methodology
    • 3 The PUPIL Framework
    • 4 Biomolecular Applications
    • 5 Recent Developments
    • 6 Conclusions
    • Acknowledgments
  • Chapter Two: Efficient Calculation of Enzyme Reaction Free Energy Profiles Using a Hybrid Differential Relaxation Algorithm: Application to Mycobacterial Zinc Hydrolases
    • Abstract
    • 1 Introduction
    • 2 Computational Methods
    • 3 Results
    • 4 Discussion
    • 5 Conclusions
    • Acknowledgments
  • Chapter Three: A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules
    • Abstract
    • 1 Introduction
    • 2 Description of the Method
    • 3 Dynamical Analysis of Reactions in Biomolecules
    • 4 Catalytic Mechanism of TIM
    • 5 Conclusions
    • Acknowledgments
  • Chapter Four: Explicit Drug Re-positioning: Predicting Novel Drug–Target Interactions of the Shelved Molecules with QM/MM Based Approaches
    • Abstract
    • 1 Introduction
    • 2 The Principle
    • 3 Subtractive QM/MM Coupling
    • 4 Additive QM/MM Coupling
    • 5 Ligand Polarization
    • 6 Protein Polarization
    • 7 QM/MM Molecular Dynamics
    • 8 Geometry Optimization
    • 9 Applications of QM/MM Methods to Structure-Based Drug Design
    • 10 Five Years View Point: Future of QM/MM-Based Repositioning
    • 11 Conclusion
    • Acknowledgments
  • Chapter Five: Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function
    • Abstract
    • 1 Introduction
    • 2 Classification of Halogenases
    • 3 General Mechanism of α-Ketoglutarate-Dependent Halogenases
    • Acknowledgments
  • Chapter Six: The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations: Applications to Enzymatic Reactions
    • Abstract
    • 1 Introduction
    • 2 Case Studies
    • 3 Conclusions
    • 4 Future Directions
    • Acknowledgments
  • Chapter Seven: QM and QM/MM Methods Compared: Case Studies on Reaction Mechanisms of Metalloenzymes
    • Abstract
    • 1 Introduction
    • 2 Advantages of QM/MM
    • 3 Disadvantages of QM/MM
    • 4 Steric Constrains in QM Versus QM/MM Approach
    • 5 Influence of the Embedding Scheme on the Reaction Chemistry: Case of EbDH
    • 6 The Size of QM-Part and the Over Polarization Effect
    • 7 How Can a Specific Enzymes Environment Alter the Intrinsic Nature of a Reaction?
    • 8 Novel Modifications in Enzyme Structures May Produce Reactivity Patterns Only Observed Using QM/MM
    • 9 Ring Hydroxylation and Rearrangement by 4-Hydroxyphenylpyruvate Dioxygenase
    • 10 Conclusions
    • Acknowledgments
  • Chapter Eight: QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism
    • Abstract
    • 1 Introduction
    • 2 Methodological Overview
    • 3 Retaining GTs Mechanism
    • 4 Conclusions
    • Acknowledgments
  • Chapter Nine: Excited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantum Mechanical and Molecular Mechanical Calculations
    • Abstract
    • 1 Introduction
    • 2 Method
    • 3 Implementation of the QM/MM Approach in Protein
    • 4 Conclusion and Perspective
  • Author Index
  • Subject Index


Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions continues the tradition of the Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists.

Each volume brings forth new information about protocols and analysis of proteins, with each thematically organized volume guest edited by leading experts in a broad range of protein-related topics.

Key Features

  • Describes advances in application of powerful techniques in the biosciences
  • Provides cutting-edge developments in protein chemistry and structural biology
  • Chapters are written by authorities in their field
  • Targeted to a wide audience of researchers, specialists, and students


Researchers and specialists in protein structure and interactions, cancer biology, psychiatry and mass spectrometry. This volume would also be of a great use to students working on projects in these areas.


No. of pages:
© Academic Press 2015
24th September 2015
Academic Press
Hardcover ISBN:
eBook ISBN:

Ratings and Reviews

About the Serial Volume Editor

Tatyana Karabencheva-Christova

Dr. Tatyana Karabencheva-Christova works at the Department of Applied Sciences, University of Northumbria, UK.

Affiliations and Expertise

Department of Chemistry, Michigan Technological University, Houghton, MI, USA