Biomolecular modelling and simulations:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier Acad. Press
2014
|
| Edition: | 1. ed. |
| Series: | Advances in protein chemistry and structural biology
96 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIV, 316 S. Ill., graph. Darst. |
| ISBN: | 9780128000137 |
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| 245 | 1 | 0 | |a Biomolecular modelling and simulations |c ed. by Tatyana Karabencheva-Christova |
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Record in the Search Index
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| adam_text | Titel: Biomolecular modelling and simulations
Autor: Karabencheva-Christova, Tatyana
Jahr: 2014
CONTENTS
Contributors ,x
Preface x/,7
1. The Interplay Between Molecular Modeling and Chemoinformatics
to Characterize Protein-Ligand and Protein-Protein Interactions
Landscapes for Drug Discovery 1
José L. Medina-Franco, Oscar Méndez-Lucio, and Karina Martinez-Mayorga
1. Introduction 2
2. Characterizing PLIs with Fingerprints 3
3. Visualization of PLIs and PLIFs: The PLIs Space 12
4. Exploring SPLIRs 17
5. Target-Ligand Relationships in Chemogenomics Data Sets 25
6. Protein-Protein Interactions 28
7. Conclusions 30
Acknowledgments 31
References 31
2. Computational Study of Putative Residues Involved
in DNA Synthesis Fidelity Checking in Thermus aquaticus
DNA Polymerase I 39
Angela A. Elias and G. Andres Cisneros
1. Introduction 40
2. Methods 42
3. Results and Discussion 46
4. Conclusions 71
References 72
3. New Strategies for Integrative Dynamic Modeling
of Macromolecular Assembly 77
Enrico Spiga, Matteo Thomas Degiacomi, and Matteo Dal Peraro
1. Introduction 78
2. Predicting Protein-Protein Recognition at the Atomistic Level 80
3. Tackling Protein-Protein Interactions at Coarse-Grained Resolution 81
4. Predicting Protein Assembly Using Integrative Modeling 91
5. Conclusions and Perspectives 101
vi
Contents
Acknowledgments 103
References 103
4. Stability of Amyloid Oligomers 113
Workalemahu M. Berhanu and Ulrich H.E. Hansmann
1. Introduction 113
2. Effect of Force Field on the Preformed Oligomer 118
3. Role of Mutations 118
4. Stability of Cylindrin ß-Barrel Amyloid Oligomer Models 120
5. Amyloid Polymorphism 122
6. Amyloid Aggregation and Cross Seeding 124
7. Toxicity Mechanism of Amyloid from Molecular Dynamic Simulations 128
8. Conclusions and Outlook 130
Acknowledgments 132
References 132
5. Recent Advances in Transferable Coarse-Grained
Modeling of Proteins 143
Parimal Kar and Michael Feig
1. Introduction 144
2. CG Models of Protein 147
3. Hybrid AII-atom/Coarse-Grained (AA/CG) Modeling of Proteins 164
4. Outlook 170
5. Conclusions 171
Acknowledgment 171
References 171
6. Studying Allosteric Regulation in Metal Sensor Proteins
Using Computational Methods 181
Dhruva K. Chakravorty and Kenneth M. Merz Jr.
1. Introduction 183
2. Methods 187
3. Understanding Protein-DNA Interactions 191
4. Flydrogen-ßonding Pathway 197
5. Quantifying Metal-Ion Mediated Allostery 205
6. Mutant Analyses to Understand the HBP 208
7. Conclusions 211
Acknowledgments 214
References 214
Contents vii
7. Insights in the Mechanism of Action and Inhibition of
N-Acylethanolamine Acid Amidase by Means
of Computational Methods 219
Alessio Lodola, Silvia Rivara, and Marco Mor
1. Introduction 220
2. General Information and Catalytic Mechanism of Cysteine Ntn-Hydrolases 221
3. Inhibition of NAAA by ß-Lactones 225
4. Recent Advances in the Field of Active-Site-Directed NAAA Inhibitors 230
Acknowledgment 232
References 232
8. CHARMM-GUI PDB Manipulator for Advanced Modeling
and Simulations of Proteins Containing Nonstandard
Residues 235
Sunhwan Jo, Xi Cheng, Shahidul M. Islam, Lei Huang, Huan Rui,
Allen Zhu, Hui Sun Lee, Yifei Qi, Wei Han, Kenno Vanommeslaeghe,
Alexander D. MacKerell Jr., Benoît Roux, and Wonpil Im
1. Introduction 236
2. Ligand FF Generation 238
3. MTS Reagents 244
4. Unnatural Amino Acids 253
5. Perspectives 259
Acknowledgments 259
References 260
9. High-Resolution Modeling of Protein Structures Based
on Flexible Fitting of Low-Resolution Structural Data 267
Wenjun Zheng and Mustafa Tekpinar
1. Introduction 268
2. Methods 270
3. Results 276
4. Discussion 279
Acknowledgment 281
References 281
Author Index
Subject Index
285
309
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| indexdate | 2024-07-10T01:24:58Z |
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| isbn | 9780128000137 |
| language | English |
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| physical | XIV, 316 S. Ill., graph. Darst. |
| publishDate | 2014 |
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| publisher | Elsevier Acad. Press |
| record_format | marc |
| series | Advances in protein chemistry and structural biology |
| series2 | Advances in protein chemistry and structural biology |
| spelling | Biomolecular modelling and simulations ed. by Tatyana Karabencheva-Christova 1. ed. Amsterdam [u.a.] Elsevier Acad. Press 2014 XIV, 316 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Advances in protein chemistry and structural biology 96 Biomolecules / Structure Biomolekül (DE-588)4135124-1 gnd rswk-swf Molekulardesign (DE-588)4265444-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Biomolekül (DE-588)4135124-1 s Molekulardesign (DE-588)4265444-0 s DE-604 Karabencheva-Christova, Tatyana Sonstige (DE-588)1044568992 oth Advances in protein chemistry and structural biology 96 (DE-604)BV035242330 96 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027995728&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Biomolecular modelling and simulations Advances in protein chemistry and structural biology Biomolecules / Structure Biomolekül (DE-588)4135124-1 gnd Molekulardesign (DE-588)4265444-0 gnd |
| subject_GND | (DE-588)4135124-1 (DE-588)4265444-0 (DE-588)4143413-4 |
| title | Biomolecular modelling and simulations |
| title_auth | Biomolecular modelling and simulations |
| title_exact_search | Biomolecular modelling and simulations |
| title_full | Biomolecular modelling and simulations ed. by Tatyana Karabencheva-Christova |
| title_fullStr | Biomolecular modelling and simulations ed. by Tatyana Karabencheva-Christova |
| title_full_unstemmed | Biomolecular modelling and simulations ed. by Tatyana Karabencheva-Christova |
| title_short | Biomolecular modelling and simulations |
| title_sort | biomolecular modelling and simulations |
| topic | Biomolecules / Structure Biomolekül (DE-588)4135124-1 gnd Molekulardesign (DE-588)4265444-0 gnd |
| topic_facet | Biomolecules / Structure Biomolekül Molekulardesign Aufsatzsammlung |
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