Computational Chemistry Methods in Structural Biology

Application of Computational Methods to the Design of Fatty Acid Amide Hydrolase (FAAH) Inhibitors Based on a Carbamic Template Structure

I. Introduction

II. Ligand-Based Drug Design

III. Structure-Based Drug Design

IV. Recent Advances

Recent theoretical and computational advances for modeling protein–ligand binding affinities

I. Introduction

II. Theory of Noncovalent Binding

III. Computational Methods

IV. Conclusions

Acknowledgment

Hybrid Schemes Based on Quantum Mechanics/Molecular Mechanics Simulations

I. Introduction: State of Art

II. Potential of Mean Force/Free-Energy Calculations

III. Applications

IV. Conclusions and Outlook

Acknowledgments

Exploring Membrane and Protein Dynamics with Dissipative Particle Dynamics

I. Introduction

II. Setting Up DPD Simulations

III. Investigating Structure and Dynamics of Membranes with DPD

Coarse-grained Representation of Protein Flexibility. Foundations, Successes, and Shortcomings

I. Introduction

II. Coarse-Grained Potentials

III. Sampling Techniques

IV. Conclusions

Recent Advances in the Molecular Modeling of Estrogen Receptor-Mediated Toxicity

I. Introduction

II. Structural Studies of the Estrogen Receptor and Its Ligands

III. Molecular Modeling Approaches to Investigate Estrogen Receptor-Mediated Toxicological Effects

IV. Molecular Modeling of Estrogen Receptor-Mediated Toxicological Effects: Case Studies

V. Conclusions

Acknowledgments

Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptors

Abbreviations

I. Introduction

II. Conformational Flexibility in GPCRs

III. Computational Approaches for Studying Conformational Ensembles of GPCRs

IV. Activation Mechanism of GPCRs

V. Concluding Remarks

Advances in Implicit Models of Water Solvent to Compute Conformational Free Energy and Molecular Dynamics of Proteins at Constant pH

I. Introduction

II. Formulation of General Implicit Solvent Model for Calculating Conformational Free Energy

III. Continuum Solvent Models

IV. Protein Ionization

V. Examples of Simulations with Implicit Solvent Models

Acknowledgments