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Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions
1st Edition, Volume 100 - September 24, 2015
Editor: Tatyana Karabencheva-Christova
Language: English
Hardback ISBN:9780128020036
9 7 8 - 0 - 1 2 - 8 0 2 0 0 3 - 6
eBook ISBN:9780128020180
9 7 8 - 0 - 1 2 - 8 0 2 0 1 8 - 0
Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions continues the tradition of the Advances in Protein Chemistry and Structural Biology…Read more
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Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions
continues the tradition of the Advancesin 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.
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.
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
No. of pages: 330
Language: English
Edition: 1
Volume: 100
Published: September 24, 2015
Imprint: Academic Press
Hardback ISBN: 9780128020036
eBook ISBN: 9780128020180
TK
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
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