Computational tools for chemical biology:
This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research....
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
London
Royal Society of Chemistry
[2018]
|
| Schriftenreihe: | Chemical biology
3 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Zusammenfassung: | This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.... |
| Beschreibung: | xiv, 377 Seiten Illustrationen, Diagramme |
| ISBN: | 9781782627005 |
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Datensatz im Suchindex
| _version_ | 1804177744399958016 |
|---|---|
| adam_text | Contents
Chapter 1 Computational Chemistry and Molecular
Modelling Basics 1
Samuel Genheden, Anna Reymer, Patricia Saenz-Mendez and
Leif A Eriksson
1 1 Introduction 1
1 2 Techniques in Biomolecular Simulations 2
121 Molecular Mechanics and Force Fields 2
122 Basic Simulation Techniques 4
123 Basic Data Analysis 8
124 Software 11
125 Examples 12
1 3 Protein Structure Prediction 13
131 Sequence Alignment and Secondary Structure Prediction 13
132 Comparative Modelling Approaches 15
133 Function Prediction 18
134 Analysing the Quality of the Modelled Structure 18
135 Software and Web Based Servers 19
1 4 Computer-based Drug Design 20
141 Pre-requisites for SBDD—Sampling Algorithms and Scoring Functions 20
142 Structure Based Drug Design (SBDD) 24
143 Ligand Based Drug Design (LBDD) 26
144 Pharmacophores 26
Chemical Biology No 3
Computational Tools for Chemical Biology
Edited by Sonsoles Martin-Santamaria
© The Royal Society of Chemistry 2018
Published by the Royal Society of Chemistry, www rsc org
vii
viii
Contents
145 Compound Optimisation 27
146 Software and Web Based Servers 29
Acknowledgements 30
References 30
Chapter 2 Molecular Dynamics Computer Simulations of Biological
Systems 39
James W Carter, Anna Sofia Tascini, John M Seddon and
Fernando Bresme
2 1 Introduction 39
2 2 The Basics of Molecular Dynamics 40
221 Force Fields for Biomolecular Simulations 41
222 Multiscale Modelling 44
223 Advanced Force Fields 45
2 3 Extracting the Information from MD 46
231 Free Energy Difference Between Two States 47
232 Enhanced Configurational Sampling 47
233 Simulating Rare Events 49
234 Computing Elastic Properties in
Biomolecular Simulations 50
2 4 MD Simulation vs Experiment 54
241 NMR and MD: Structure and Dynamics 55
242 Structure of Biomolecules and Diffraction:
Solving the Phase Problem with MD 57
2 5 Future Directions 58
2 6 Conclusion 61
Acknowledgements 63
References 63
Chapter 3 Designing Chemical Tools with Computational Chemistiy 69
Silvia Rinaldi and Giorgio Colombo
3 1 Introduction 69
3 2 Structure Based Approaches for Chemical Biology 72
3 3 Structural Dynamics as a Source of Novel Chemical
Tools 74
3 4 Combining Bioinformatics, Chemoinformatics and
Structural Information to Explore Protein Functions 79
3 5 Deep Networks and Big Data in the Discovery of
New Drugs and Chemical Tools 81
3 6 Conclusions and Perspectives 83
References 84
Contents
ix
Chapter 4 Computational Design of Protein Function 87
Marc Garcia-Borras, Kendall N Houk and
Gonzalo Jimenez-Oses
4 1 Introduction 87
4 2 The ‘Inside-out’ Design Protocol 89
421 Description of the Method 89
422 Enzymes Designed Though the ‘Inside-out’
Approach: Kemp Eliminases 92
4 3 QM/MM Approaches to Enzyme Design 94
431 Description of the Methods 94
432 Engineered Butyiylcholinesterase for
Cocaine Detoxification 96
433 Electron Transfer Reactions Catalysed by
Metalloproteins 99
4 4 Summary and Outlook 101
Acknowledgements 102
References 102
Chapter 5 Computational Enzymology: Modelling Biological Catalysts 108
Laura Masgrau, Angels Gonzalez-Lafont and Jose M Lluch
5 1 Introduction
5 2 General Framework
521 The Transition State and the Energy Barrier
522 Quantum Mechanics Molecular Mechanics
(QM/MM) Methods
5 3 Building the Model(s) of the Enzyme-Substrate
Complex(es)
531 Starting Structure and System Setup
532 Molecular Dynamics Simulations
5 4 Potential Energy Methods
541 Reaction Path Calculation
542 Transition State Localisation
543 Analysis
5 5 Free Energy Simulations
551 Umbrella Sampling Method
552 Free Energy Perturbation Theory
553 String Method: Minimum Free Energy Paths
5 6 Calculation of the Reaction Rate Constant
561 Ensemble-averaged Variational Transition
State Theory with Multi-dimensional
Tunnelling (EA-VTST/MT)
108
109
109
110
114
114
114
115
115
117
118
122
123
127
132
136
136
X
Contents
5 7 Further Considerations about the Relationship
between the Activation Free Energy and the
Extension of the Sampling of the Configurational
Space 139
References 141
Chapter 6 Computational Chemistiy Tools in Glycobiology:
Modelling of Carbohydrate-Protein Interactions 145
Alessandra Lacetera, M Alvaro Berbis, Alessandra Nurisso,
Jesus Jimenez-Barbero and Sonsoles Martm-Santamaria
6 1 What are the Carbohydrates? 145
6 2 From Mono to Polysaccharides: An Overview
of the Increasing Complexity 147
621 Monosaccharides 147
622 Disaccharides: The Glycosidic Linkage and
the Fxo-anomeric Effect 148
623 Studying the Conformations Around the
Glycosidic Linkage 149
624 Oligosaccharides 149
625 N-glycans 150
626 Polysaccharides 150
6 3 Computational Methodologies for the Study of
Carbohydrates 151
6 4 Force Fields for Carbohydrates 153
6 5 Modelling Carbohydrate-Protein
Interactions 155
6 6 Conclusions 159
Acknowledgements 159
References 159
Chapter 7 Molecular Modelling of Nucleic Acids 165
Hansel Gömez, Jürgen Walther, Leonardo Darre, Ivan Ivani,
Pablo D Dans and Modesto Orozco
7 1 Introduction 165
7 2 QM Methods 166
721 Basic Methodological Description 166
722 Examples of Use 167
7 3 Hybrid QM/MM 167
731 Basic Methodological Description 167
732 Examples of Use 168
Contents
xi
7 4 Atomistic Force-field Simulations 170
741 Basic Methodological Description 170
742 Force-field Refinements 172
743 Recent Examples of Force-field Studies of
Nucleic Acids 175
7 5 The Coarse-grain Approach 177
751 Basic Methodological Description 178
752 Coarse-grained Methods for Predicting RNA
Structures 182
7 6 Mesoscopic Models 184
761 Basic Methodological Description 185
762 Nucleosome Fibre Simulations 186
763 Chromosome Simulations 187
7 7 Conclusions 188
Acknowledgements 188
References 189
Chapter 8 Uncovering GPCR and G Protein Function by Protein
Structure Network Analysis 198
Francesca Fanelli and Angelo Felline
8 1 Introduction 198
8 2 Experimental 201
821 Materials 201
822 Methods 201
8 3 Results and Discussion 205
831 Modelling Allosteric Communication
in GPCRs 205
832 Modelling Allosteric Communication
in G Proteins 213
8 4 Conclusions 216
Acknowledgements 216
References 217
Chapter 9 Current Challenges in the Computational Modelling
of Molecular Recognition Processes 221
Lucia Perez-Regidor, Joan Guzman-Caldentey,
Carlos F Rodriguez, Jean-Marc Billod, Juan Nogales and
Sonsoles Martin-Santamaria
9 1 Modelling the Dynamics of the Proteins 221
9 2 Three-dimensional Structure Prediction and
Homology Modelling 224
xii
Contents
9 3 Modelling of Protein-Protein Interactions 225
9 4 Prediction of Protein-Protein Interactions:
Docking 226
9 5 Computational Studies of Complex
Protein Systems 229
9 6 Computational Modelling of Nanostructures 232
961 Modelling of Gold Nanoparticles 233
962 Modelling of Nanowires 234
963 Modelling of Nanotubes 235
964 Modelling of Nanomachines 236
9 7 Models of Signalling Networks 237
Acknowledgements 240
References 240
Chapter 10 Novel Insights into Membrane Transport from
Computational Methodologies 247
Victoria Oakes and Carmen Domene
10 1 Introduction 247
10 2 Computational Methods 248
10 3 Unassisted Diffusion Across Lipid Bilayers 252
10 4 Passive Transport by Ion Channels 255
10 5 Facilitated Diffusion by Transporters 259
10 6 Signalling via Receptors 264
10 7 Conclusions 268
Acknowledgements 268
References 269
Chapter 11 Application of Molecular Modelling to Speed-up the Lead
Discoveiy Process 281
Iuni M L Trist, Maurizio Botta and Anna Lucia Fallacara
11 1 Introduction 281
11 1 1 The ‘Pharmaceutical Crisis’ 281
11 1 2 The Drug Discoveiy Process 282
11 1 3 The Contribution of Molecular Modelling
to Improve Drug Discoveiy 284
11 1 4 Quantum and Molecular Mechanics in
Drug Design 285
11 1 5 An Introduction to Structure- and
Ligand-based Molecular Modelling 285
Contents
xiii
11 2 Structure-based Molecular Modelling 286
11 2 1 Sources of 3D Structures 286
11 2 2 Docking 289
11 2 3 De Novo Drug Design 291
11 2 4 Introducing Dynamics 293
11 3 Ligand-based Molecular Modelling 296
11 3 1 Similarity Searching: Same Shape,
Same Activity 297
11 3 2 Pharmacophore Modelling 299
11 3 3 QSAR 300
11 3 4 Use of In Silico Ligand-based Approaches:
A Practical Case Study on Antitubercular
Agents 304
11 4 Conclusions 305
Abbreviations 306
Acknowledgements 307
References 307
Chapter 12 Molecular Modelling and Simulations Applied to
Challenging Drug Discoveiy Targets 317
Marco De Vivo, Matteo Masetti and Giulia Rossetti
12 1 Introduction 317
12 2 Deciphering Metalloenzyme Catalysis via
Computations 319
12 2 1 Ribonuclease H 319
12 2 2 Epoxide hydrolase 321
12 3 Simulating Membrane Proteins 323
12 3 1 Membrane Enzymes: The Case of FAAH 323
12 3 2 Ion Channels: The Case of the Kvll l
Channel 324
12 3 3 GPCR: The Case of the Human Adenosine
Receptor A2A Embedded in Neuronal-like
Membrane 328
12 4 Tackling Target Flexibility Through
Simulations 331
12 4 1 Lactate Dehydrogenase 331
12 4 2 Intrinsically Disordered Proteins 333
12 4 3 Targeting RNA in Trinucleotide
Repeats Diseases 335
12 5 Conclusions 338
References 338
xiv Contents
Chapter 13 The Polypharmacology Gap Between Chemical Biology and
Drug Discovery 349
Albert A Antolin and Jordi Mestres
13 1 Introduction: Chemical Biology and the Limits
of Reductionism 349
13 1 1 Polypharmacology in Drug Discovery 349
13 1 2 Selectivity in Chemical Biology 351
13 2 Systems Pharmacology: Databases and Methods 353
13 2 1 Databases of Chemical, Biological and
Pharmacological Data 353
13 2 2 Computational Methods to Predict
Polypharmacology 354
13 3 Case Study 1: The Impact of Chemical Probe
Polypharmacology on PARP Drug Discovery 355
13 3 1 The History of PARP Biology: From Probes
to Drugs 355
13 3 2 PJ34: A PARP Chemical Tool Binding to
PIM Kinases 357
13 3 3 Differential Off-target Kinase
Pharmacology Between Clinical PARP
Inhibitors 360
13 4 Case Study 2: Distant Off-target Pharmacology
among MLP Chemical Probes 363
13 5 Conclusions and Outlook 365
Acknowledgements 366
References 366
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| indexdate | 2024-07-10T07:52:57Z |
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| isbn | 9781782627005 |
| language | English |
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| spelling | Martín-Santamaría, Sonsoles (DE-588)1144908191 edt Computational tools for chemical biology edited by Sonsoles Martín-Santamaría, Center for Biological Research, CIB-CSIC, Madrid, Spain London Royal Society of Chemistry [2018] © 2018 xiv, 377 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Chemical biology 3 This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.... Computational biology Biochemistry Data processing Molecules Models Biochemical Phenomena Computational Biology Models, Chemical Models, Biological Biochemistry Molecules Chemische Biologie (DE-588)7657972-4 gnd rswk-swf Wissenschaftlich-technische Software (DE-588)4753754-1 gnd rswk-swf Biochemie (DE-588)4006777-4 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Chemische Biologie (DE-588)7657972-4 s Biochemie (DE-588)4006777-4 s Bioinformatik (DE-588)4611085-9 s Wissenschaftlich-technische Software (DE-588)4753754-1 s DE-188 Erscheint auch als Online-Ausgabe, PDF 978-1-78801-013-9 Erscheint auch als Online-Ausgabe, EPUB 978-1-78801-256-0 Chemical biology 3 (DE-604)BV044309025 3 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029838815&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Computational tools for chemical biology Chemical biology Computational biology Biochemistry Data processing Molecules Models Biochemical Phenomena Computational Biology Models, Chemical Models, Biological Biochemistry Molecules Chemische Biologie (DE-588)7657972-4 gnd Wissenschaftlich-technische Software (DE-588)4753754-1 gnd Biochemie (DE-588)4006777-4 gnd Bioinformatik (DE-588)4611085-9 gnd |
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| title | Computational tools for chemical biology |
| title_auth | Computational tools for chemical biology |
| title_exact_search | Computational tools for chemical biology |
| title_full | Computational tools for chemical biology edited by Sonsoles Martín-Santamaría, Center for Biological Research, CIB-CSIC, Madrid, Spain |
| title_fullStr | Computational tools for chemical biology edited by Sonsoles Martín-Santamaría, Center for Biological Research, CIB-CSIC, Madrid, Spain |
| title_full_unstemmed | Computational tools for chemical biology edited by Sonsoles Martín-Santamaría, Center for Biological Research, CIB-CSIC, Madrid, Spain |
| title_short | Computational tools for chemical biology |
| title_sort | computational tools for chemical biology |
| topic | Computational biology Biochemistry Data processing Molecules Models Biochemical Phenomena Computational Biology Models, Chemical Models, Biological Biochemistry Molecules Chemische Biologie (DE-588)7657972-4 gnd Wissenschaftlich-technische Software (DE-588)4753754-1 gnd Biochemie (DE-588)4006777-4 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Computational biology Biochemistry Data processing Molecules Models Biochemical Phenomena Computational Biology Models, Chemical Models, Biological Biochemistry Molecules Chemische Biologie Wissenschaftlich-technische Software Biochemie Bioinformatik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029838815&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV044309025 |
| work_keys_str_mv | AT martinsantamariasonsoles computationaltoolsforchemicalbiology |