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05055nam a2200541 4500 |
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ocn925780014 |
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OCoLC |
| 005 |
20180501122027.0 |
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m o d |
| 007 |
cr cnu---unuuu |
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151021s2015 maua o 001 0 eng d |
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|a OPELS
|b eng
|e rda
|e pn
|c OPELS
|d OCLCO
|d OCLCF
|d OCLCO
|d N$T
|d EBLCP
|d IDEBK
|d YDXCP
|d N$T
|d OCLCO
|d CDX
|d OCLCO
|d UAB
|d OCLCQ
|d MEU
|d NLE
|d GrThAP
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|a 928483574
|a 929522853
|a 931504248
|a 932329900
|a 945763324
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|a 9780128020180
|q electronic bk.
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|a 0128020180
|q electronic bk.
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|a 9780128020036
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|a 0128020032
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|a (OCoLC)925780014
|z (OCoLC)928483574
|z (OCoLC)929522853
|z (OCoLC)931504248
|z (OCoLC)932329900
|z (OCoLC)945763324
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| 050 |
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4 |
|a QD431
|b .A3 v. 100eb
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| 072 |
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7 |
|a SCI
|x 013050
|2 bisacsh
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0 |
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|a 541/.28
|2 23
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|a TEFA
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|a Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions /
|c edited by Tatyana Karabencheva-Christova.
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| 264 |
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1 |
|a Waltham, MA :
|b Academic Press,
|c 2015.
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| 300 |
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|a 1 online resource (xv, 313 pages :
|b illustrations).
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| 336 |
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|a text
|b txt
|2 rdacontent
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| 337 |
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|a computer
|b c
|2 rdamedia
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| 338 |
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|a online resource
|b cr
|2 rdacarrier
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| 490 |
1 |
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|a Advances in protein chemistry and structural biology ;
|v volume 100
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| 546 |
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|a Text in English.
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| 500 |
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|a Includes indexes.
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| 588 |
0 |
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|a Print version record.
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0 |
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|a Front Cover; Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions; Copyright; Contents; Contributors; Preface; Acknowledgments; Chapter One: PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecula ...; 1. Introduction; 2. QM/MM-MD Methodology; 3. The PUPIL Framework; 3.1. Features; 3.1.1. High Performing Computing; 3.2. User Interface; 3.2.1. QM Program and Method Selection; 3.2.2. QM Region Selection Rules; 3.3. Technical Details; 4. Biomolecular Applications; 5. Recent Developments
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| 505 |
8 |
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|a 5.1. Working with Multiple Active Zones5.2. Treatment of Long-Range Electrostatic Interactions; 6. Conclusions; Acknowledgments; References; Chapter Two: Efficient Calculation of Enzyme Reaction Free Energy Profiles Using a Hybrid Differential Relaxation Algorit...; 1. Introduction; 1.1. Free Energy Profiles of Enzymatic Reactions; 1.1.1. MSMD and Jarzynskiś Relationship; 1.1.2. Hybrid Differential Relaxation Algorithm; 1.2. Mycobacterium tuberculosis Zinc Hydrolases; 1.2.1. MshB (Rv1170); 1.2.2. MA-Amidase (Rv3717); 1.2.3. Zn Hydrolases Reaction Mechanism; 2. Computational Methods
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8 |
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|a 2.1. Theoretical Basis of HyDRA2.2. Starting Structures; 2.2.1. MshB; 2.2.2. MA-Amidase; 2.3. Classical, DFT, and QM/MM Simulation Parameters; 2.4. Free Energy Determination Simulation Strategy and Parameters; 2.4.1. Reaction Coordinate Definition; 2.4.2. MSMD Trajectories and Pulling Speed; 3. Results; 3.1. Mtb Zinc Hydrolases Display a Flexible Zinc Coordination Sphere; 3.2. Hydroxide Ion Generation Step; 3.3. Hydroxide Attack to Amide Carbonyl; 3.3.1. Effect of DRAr; 3.3.2. Detailed Mechanistic and Comparative Analysis Between MshB and MA-Amidase
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8 |
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|a 3.3.3. Role of Substrate Carbonyl Coordination3.4. C-N Amide Bond Breaking; 3.4.1. Stability of Tetrahedral Intermediate; 3.4.2. FEPs of the C-N Bond Breaking Step; 3.5. Alternative Mechanisms; 4. Discussion; 4.1. The Complete Mechanism of MshB and MA-Amidase Zn Hydrolases; 4.2. Role of the Zn Ion in Catalysis; 4.3. Comparison with Other Zn Hydrolases; 4.4. Convergent Structural Evolution of Zn Hydrolases; 4.5. Final Remark on QM/MM Studies of Enzyme Reaction Mechanisms; 5. Conclusions; Acknowledgments; References
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| 505 |
8 |
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|a Chapter Three: A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules1. Introduction; 2. Description of the Method; 2.1. QM Method: Fireball; 2.2. Fireball/Amber; 3. Dynamical Analysis of Reactions in Biomolecules; 4. Catalytic Mechanism of TIM; 4.1. Introduction; 4.2. Results; 4.3. Discussion; 5. Conclusions; Acknowledgments; References; Chapter Four: Explicit Drug Re-positioning: Predicting Novel Drug-Target Interactions of the Shelved Molecules with QM/MM ...; 1. Introduction; 2. The Principle; 3. Subtractive QM/MM Coupling
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| 650 |
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0 |
|a Quantum chemistry.
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| 650 |
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0 |
|a Biomolecules
|x Analysis.
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| 650 |
|
7 |
|a Biomolecules
|x Analysis.
|2 fast
|0 (OCoLC)fst00832625
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| 650 |
|
7 |
|a Quantum chemistry.
|2 fast
|0 (OCoLC)fst01085086
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| 650 |
|
7 |
|a SCIENCE / Chemistry / Physical & Theoretical
|2 bisacsh
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| 655 |
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4 |
|a Electronic books.
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| 655 |
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0 |
|a Electronic books.
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| 700 |
1 |
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|a Karabencheva-Christova, Tatyana,
|e editor.
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| 776 |
0 |
8 |
|i Print version:
|t Combined quantum mechanical and molecular mechanical modelling of biomolecular interactions
|z 9780128020036
|w (OCoLC)911073447
|
| 830 |
|
0 |
|a Advances in protein chemistry and structural biology ;
|v v. 100.
|
| 856 |
4 |
0 |
|u https://www.sciencedirect.com/science/bookseries/18761623/100
|z Full Text via HEAL-Link
|
