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Quantum chemical study of molecular recognition in protein-ligand complexes
Table of Contents
Abstract
Acknowledgements
Table of Contents
Lists of Tables
List of Figures
1 Introduction
2 Theory and Methods
2.1 Electronic Structure Theory
2.2 Density Functional Theory (DFT)
2.3 Level of Theory and Basis Set
2.4 Molecular Mechanics (MM)
2.5 The Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Method
2.6 Solvation Models
2.7 Intermolecular Interaction Energy
2.7.1 Interaction Energy in Gas Phase
2.7.2 Interaction Energy in Solution
3 Quantum Chemical Analysis of Non-Nucleoside Reverse Transcriptase Inhibitors in HIV-1 Reverse Transcriptase
3.1 Introduction
3.2 Methods
3.3 Results and Discussion
3.3.1 Binding Pocket of Efavirenz and Nevirapine
3.3.2 Interaction Energies between NEV, EFZ and the Wild-type RT
3.3.3 Correlation with Clinically Observed Drug-Resistant Mutations
3.3.4 Interaction Energies between NEV, EFZ and K103N, Y181C Mutants of HIV-1 Reverse Transcriptase
3.4 Summary
4 CH-π Interactions with Adenine in ATP-binding Proteins
4.1 Introduction
4.2 Methods
4.3 Results and Discussion
4.3.1 Alignment of Adenine-Protein Complexes
4.3.2 Intermolecular Interaction Energies
4.4 Summary
5 A Hybrid Quantum Mechanics/Molecular Mechanics Optimization of a Ligand-Protein Complex between Rapamycin Analogues and FKBP12
5.1 Introduction
5.2 Methods
5.3 Results and Discussion
5.3.1 Modeling Rapalogs into the Binding Pocket
5.3.2 A Hybrid QM/MM Optimization of the FKBP12-Rapalog Complexes
5.4 Summary
References Bài viết liên quan
