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Biomolecular Modelling and Simulations
- 1st Edition, Volume 96 - September 30, 2014
- Editor: Tatyana Karabencheva-Christova
- Language: English
- Hardback ISBN:9 7 8 - 0 - 1 2 - 8 0 0 0 1 3 - 7
- eBook ISBN:9 7 8 - 0 - 1 2 - 8 0 0 7 8 9 - 1
Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new in… Read more
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Request a sales quotePublished continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics.
- Describes advances in biomolecular modelling and simulations
- Chapters are written by authorities in their field
- Targeted to a wide audience of researchers, specialists, and students
- The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables
researchers, specialists in 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
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
- No. of pages: 330
- Language: English
- Edition: 1
- Volume: 96
- Published: September 30, 2014
- Imprint: Academic Press
- Hardback ISBN: 9780128000137
- eBook ISBN: 9780128007891
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, USARead Biomolecular Modelling and Simulations on ScienceDirect