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Biomolecular modelling and simulations /
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...
| Clasificación: | Libro Electrónico |
|---|---|
| Otros Autores: | |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Oxford :
Academic Press/Elsevier,
2014.
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| Colección: | Advances in protein chemistry and structural biology ;
Volume 96. |
| Temas: | |
| Acceso en línea: | Texto completo Texto completo |
Tabla de Contenidos:
- Front Cover; Biomolecular Modelling and Simulations; Copyright; Contents; Contributors; Preface; References; Chapter 1: The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein-Ligand and Protein-Prote ... ; 1. Introduction; 2. Characterizing PLIs with Fingerprints; 3. Visualization of PLIs and PLIFs: The PLIs Space; 3.1. 2D Schematic diagrams of PLIs; 3.2. Representation and application of PLIFs as 3D pharmacophore models; 3.3. Visualization of PLIFs using the concept of chemical space; 4. Exploring SPLIRs; 4.1. Activity landscape: Activity cliffs and hot spots.
- 4.2. 3D Activity Cliffs4.3. Structure-based activity cliffs and hot spots; 4.4. Activity cliff generators and structural interpretation; 4.5. Interaction cliffs; 5. Target-Ligand Relationships in Chemogenomics Data Sets; 5.1. Analyzing chemogenomic sets using target-ligand networks; 5.2. Proteochemometric modeling; 6. Protein-Protein Interactions; 7. Conclusions; Acknowledgments; References; Chapter Two: Computational Study of Putative Residues Involved in DNA Synthesis Fidelity Checking in Thermus aquaticus DN ... ; 1. Introduction; 2. Methods; 2.1. Preparation of crystal structures.
- 2.2. MD simulations2.3. NCI calculations; 2.4. Energy decomposition analysis; 2.5. EFER analysis; 3. Results and Discussion; 4. Conclusions; References; Chapter Three: New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly; 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; References; Chapter Four: Stability of Amyloid Oligomers; 1. Introduction.
- 2. Effect of Force Field on the Preformed Oligomer3. Role of Mutations; 4. Stability of Cylindrin �-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; References; Chapter Five: Recent Advances in Transferable Coarse-Grained Modeling of Proteins; 1. Introduction; 2. CG Models of Protein; 2.1. UNRES model; 2.2. MARTINI model; 2.3. OPEP model; 2.4. SCORPION model; 2.5. PaLaCe model; 2.6. Bereau and Deserno model; 2.7. PRIMO model.
- 2.8. GBEMP model2.9. PRIME model; 3. Hybrid All-atom/Coarse-Grained (AA/CG) Modeling of Proteins; 3.1. PACE model; 3.2. ATTRACT model; 3.3. Promising hybrid models; 4. Outlook; 5. Conclusions; Acknowledgment; References; Chapter Six: Studying Allosteric Regulation in Metal Sensor Proteins Using Computational Methods; 1. Introduction; 2. Methods; 2.1. Classical MD simulations; 2.1.1. Metal ion force fields; 2.1.2. Preparing the proteins for simulation; 2.1.3. Simulation protocols; 2.2. QM/MM and QM/MM MD calculations; 3. Understanding Protein-DNA Interactions.