Biomolecular Modelling and Simulations

Preface

1: The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery
Abstract

1 Introduction

2 Characterizing PLIs with Fingerprints

3 Visualization of PLIs and PLIFs: The PLIs Space

4 Exploring SPLIRs

5 Target–Ligand Relationships in Chemogenomics Data Sets

6 Protein–Protein Interactions

7 Conclusions
Acknowledgments

2: Computational Study of Putative Residues Involved in DNA Synthesis Fidelity Checking in Thermus aquaticus DNA Polymerase I
Abstract

1 Introduction

2 Methods

3 Results and Discussion

4 Conclusions

3: New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Abstract

1 Introduction

2 Predicting Protein–Protein Recognition at the Atomistic Level

3 Tackling Protein–Protein Interactions at Coarse-Grained Resolution

4 Predicting Protein Assembly Using Integrative Modeling

5 Conclusions and Perspectives
Acknowledgments

4: Stability of Amyloid Oligomers
Abstract

1 Introduction

2 Effect of Force Field on the Preformed Oligomer

3 Role of Mutations

4 Stability of Cylindrin β-Barrel Amyloid Oligomer Models

5 Amyloid Polymorphism

6 Amyloid Aggregation and Cross Seeding

7 Toxicity Mechanism of Amyloid from Molecular Dynamic Simulations

8 Conclusions and Outlook
Acknowledgments

5: Recent Advances in Transferable Coarse-Grained Modeling of Proteins
Abstract

1 Introduction

2 CG Models of Protein

3 Hybrid All-atom/Coarse-Grained (AA/CG) Modeling of Proteins

4 Outlook

5 Conclusions
Acknowledgment

6: Studying Allosteric Regulation in Metal Sensor Proteins Using Computational Methods
Abstract

1 Introduction

2 Methods

3 Understanding Protein–DNA Interactions

4 Hydrogen-Bonding Pathway

5 Quantifying Metal-Ion Mediated Allostery

6 Mutant Analyses to Understand the HBP

7 Conclusions
Acknowledgments

7: Insights in the Mechanism of Action and Inhibition of N-Acylethanolamine Acid Amidase by Means of Computational Methods
Abstract

1 Introduction

2 General Information and Catalytic Mechanism of Cysteine Ntn-Hydrolases

3 Inhibition of NAAA by β-Lactones

4 Recent Advances in the Field of Active-Site-Directed NAAA Inhibitors
Acknowledgment

8: CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues
Abstract

1 Introduction

2 Ligand FF Generation

3 MTS Reagents

4 Unnatural Amino Acids

5 Perspectives
Acknowledgments

9: High-Resolution Modeling of Protein Structures Based on Flexible Fitting of Low-Resolution Structural Data
Abstract

1 Introduction

2 Methods

3 Results

4 Discussion
Acknowledgment
Author Index
Subject Index