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Biomolecular Modelling and Simulations
1st Edition, Volume 96 - September 30, 2014
Editor: Tatyana Karabencheva-Christova
Language: English
Hardback ISBN:9780128000137
9 7 8 - 0 - 1 2 - 8 0 0 0 1 3 - 7
eBook ISBN:9780128007891
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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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 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
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, USA
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