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Molecular Modeling: Basic Principles and Applications 3rd edition [Mīkstie vāki]

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(Swiss Institute of Technology (ETH), Zürich, Switze), (University of Duesseldorf, Germany), (University of Halle-Wittenberg, Germany), (University of Strasbourg, France)
  • Formāts: Paperback / softback, 320 pages, height x width x depth: 241x170x18 mm, weight: 608 g
  • Izdošanas datums: 16-Jan-2008
  • Izdevniecība: Blackwell Verlag GmbH
  • ISBN-10: 3527315683
  • ISBN-13: 9783527315680
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Molecular Modeling: Basic Principles and Applications 3rd editionPalielināt
  • Formāts: Paperback / softback, 320 pages, height x width x depth: 241x170x18 mm, weight: 608 g
  • Izdošanas datums: 16-Jan-2008
  • Izdevniecība: Blackwell Verlag GmbH
  • ISBN-10: 3527315683
  • ISBN-13: 9783527315680
Citas grāmatas par šo tēmu:
Permanent link: https://www.kriso.lv/db/9783527315680.html
Keywords:
Ideal for beginners, this book explains the basics of modeling in a competent yet easily understandable way. Following complete sections on the modeling of small molecules, protein modeling and chemogenomics, completely worked-out examples show the way to the reader's first modeling experiment.

This new, third edition features a new chapter on chemogenomics, reflecting the trend towards 'chemical biology', as well as the protein modeling example being completely rewritten for a better 'feel' of modeling complex biomolecules.

The authors are experienced university teachers who regularly hold courses on molecular modeling, making this a tried-and-tested text for teachers. It is equally valuable for experts, since it is the only book to evaluate the strengths and limitations of the molecular modeling techniques and software currently available.

Recenzijas

"Beginners as well as experts in the field of biochemistry, molecular biology, and drug development will find this book quite handy and useful. The third edition is justified given the rapid development of hardware and software tools and other advances in the applications of molecular modeling techniques." (Doody's, April 2009) "The authors are experienced university lecturers and as a result of their teaching practices the textbook provides teachers with a tried-and-tested learning material. The text is equally valuable to experts" (International Journal of Bioautomation, April 2009)

"An excellent resource as an introduction to molecular modelling techniques .I can particularly recommend this book to academics." (Journal of Medicinal Chemistry, September 2008)

Preface to the Third Edition x
Introduction
1(8)
Modern History of Molecular Modeling
2(1)
Do Today's Molecular Modeling Methods Only Make Pictures of the Lukretian World or Do They Make Anything More?
3(1)
What are Models Used For?
4(1)
Molecular Modeling Uses all Four Kinds for Model Building
5(1)
The Final Step Is Design
5(1)
Scope of the Book
6(3)
Small Molecules
9(84)
Generation of 3D Coordinates
9(7)
Crystal Data
9(1)
Fragment Libraries
10(2)
Conversion of 2D Structural Data into 3D Form
12(3)
References
15(1)
Computational Tools for Geometry Optimization
16(16)
Force Fields
16(3)
Geometry Optimization
19(2)
Energy-minimizing Procedures
21(2)
Use of Charges, Solvation Effects
23(1)
Quantum Mechanical Methods
24(5)
References
29(3)
Conformational Analysis
32(18)
Conformational Analysis Using Systematic Search Procedures
34(3)
Conformational Analysis Using Monte Carlo Methods
37(2)
Conformational Analysis Using Molecular Dynamics
39(5)
Which Is the Method of Choice?
44(2)
References
46(4)
Determination of Molecular Interaction Potentials
50(19)
Molecular Electrostatic Potentials (MEPs)
50(7)
Molecular Interaction Fields
57(9)
Display of Properties on a Molecular Surface
66(1)
References
66(3)
Further Reading
69(8)
Pharmacophore Identification
70(1)
Molecules to be Matched
70(2)
Atom-by-atom Superposition
72(2)
Superposition of Molecular Fields
74(1)
References
75(2)
3D QSAR Methods
77(16)
The CoMFA Method
77(4)
Other CoMFA-related Methods
81(2)
More 3D QSAR Methods
83(1)
Receptor-based 3D QSAR
84(2)
Reliability of 3D QSAR Models
86(1)
References
87(4)
Further Reading
91(2)
A Case Study for Small Molecule Modeling: Dopamine D3 Receptor Antagonists
93(18)
A Pharmacophore Model for Dopamine D3 Receptor Antagonists
93(11)
The Aromatic--Basic Fragment
99(1)
The Spacer
100(1)
The Aromatic--Amidic Residue
101(1)
Resulting Pharmacophore
102(1)
Molecular Interaction Fields
102(2)
3D QSAR Analysis
104(7)
Variable Reduction and PLS Model
104(3)
Validation of the Model
107(1)
Prediction of External Ligands
108(2)
References
110(1)
Introduction to Comparative Protein Modeling
111(70)
Where and How to Get Information on Proteins
111(5)
References
115(1)
Terminology and Principles of Protein Structure
116(10)
Conformational Properties of Proteins
116(3)
Types of Secondary Structural Elements
119(3)
Homologous Proteins
122(2)
References
124(2)
Comparative Protein Modeling
126(23)
Procedures for Sequence Alignments
127(6)
Determination and Generation of Structurally Conserved Regions (SCRs)
133(2)
Construction of Structurally Variable Regions (SVRs)
135(1)
Side-Chain Modeling
136(2)
Distance Geometry Approach
138(1)
Secondary Structure Prediction
139(2)
Threading Methods
141(3)
References
144(5)
Optimization Procedures -- Model Refinement -- Molecular Dynamics
149(9)
Force Fields for Protein Modeling
149(1)
Geometry Optimization
150(1)
The Use of Molecular Dynamics Simulations in Model Refinement
151(2)
Treatment of Solvated Systems
153(2)
Ligand-binding Site Complexes
155(1)
References
155(3)
Validation of Protein Models
158(15)
Stereochemical Accuracy
158(6)
Packing Quality
164(2)
Folding Reliability
166(3)
References
169(4)
Properties of Proteins
173(8)
Electrostatic Potential
173(4)
Interaction Potentials
177(1)
Hydrophobicity
177(1)
References
178(3)
Virtual Screening and Docking
181(36)
Preparation of the Partners
181(8)
Preparation of the Compound Library
181(5)
Representation of Proteins and Ligands
186(3)
Docking Algorithms
189(7)
Incremental Construction Methods
189(2)
Genetic Algorithms
191(1)
Tabu Search
192(2)
Simulated Annealing and Monte Carlo Simulations
194(1)
Shape-fitting Methods
195(1)
Miscellaneous Approaches
195(1)
Scoring Functions
196(4)
Empirical Scoring Functions
196(2)
Force-field-based Scoring Functions
198(1)
Knowledge-based Scoring Functions
198(1)
Critical Overview of Fast Scoring Functions
199(1)
Postfiltering Virtual Screening Results
200(2)
Filtering by Topological Properties
200(1)
Filtering by Consensus Mining Approaches
200(1)
Filtering by Combining Computational Procedures
201(1)
Filtering by Chemical Diversity
201(1)
Filtering by Visual Inspection
202(1)
Comparison of Different Docking and Scoring Methods
202(1)
Examples of Successful Virtual Screening Studies
203(3)
Outlook
206(11)
References
207(10)
Scope and Limits of Molecular Docking
217(16)
Docking in the Polar Active Site that Contains Water Molecules
218(7)
Including Cofactor in Docking?
225(2)
Impact of Tautomerism on Docking
227(6)
References
229(2)
Further Reading
231(2)
Chemogenomic Approaches to Rational Drug Design
233(32)
Description of Ligand and Target Spaces
235(7)
Ligand Space
236(2)
Target Space
238(2)
Protein--Ligand Space
240(2)
Ligand-based Chemogenomic Approaches
242(7)
Annotating Ligand Libraries
242(2)
Privileged Structures
244(2)
Ligand-based In silico Screening
246(3)
Target-based Chemogenomic Approaches
249(5)
Sequence-based Comparisons
249(2)
Structure-based Comparisons
251(3)
Target-Ligand-based Chemogenomic Approaches
254(4)
Chemical Annotation of Target Binding Sites
254(2)
Two-dimensional Searches
256(1)
Three-dimensional Searches
256(2)
Concluding Remarks
258(7)
References
258(7)
A Case Study for Protein Modeling: the Nuclear Hormone Receptor CAR as an Example for Comparative Modeling and the Analysis of Protein-Ligand Complexes
265(34)
The Biochemical and Pharmacological Description of the Problem
265(3)
Nuclear Hormone Receptor Superfamily
265(1)
Molecular Architecture and Activation Mechanisms of Nuclear Hormone Receptors
265(2)
The Human Constitutive Active Androstan Receptor (CAR)
267(1)
CAR Ligands
267(1)
Comparative Modeling of the Human Nuclear Hormone Receptor CAR
268(4)
Choosing Appropriate Template Structures
269(2)
Homology Modeling of the Human CAR
271(1)
Setting up the System for the Molecular Dynamics Simulations
271(1)
Analysis of the Models that Emerged from MD Simulations
272(7)
Atomic Fluctuations
272(3)
AF-2 Interaction Domain
275(1)
Deciphering the Structural Basis for Constitutive Activity of Human CAR
276(2)
Coactivator Binding
278(1)
Analysis of CAR Mutants
279(5)
Identifying Important Amino Acids for CAR Activation
279(3)
MD Simulations of Selected CAR Mutants
282(2)
Modeling of CAR-Ligand Complexes
284(2)
The CAR X-ray Structure Comes into Play
286(6)
How Accurate is the Generated CAR Model?
286(2)
Docking Studies Using the CAR X-ray Structure
288(1)
The Basis for Constitutive Activity Revisited
289(3)
Virtual Screening for Novel CAR Activators
292(3)
Concluding Remarks
295(4)
References
296(3)
Index 299
Hans-Dieter Holtje is director of the Institute of Pharmaceutical Chemistry at the Heinrich-Heine-Universitat Dusseldorf (Germany) where he also holds the chair of Medicinal Chemistry. His main interest is the molecular mechanism of drug action.

Wolfgang Sippl is Professor of Pharmaceutical Chemistry at the Martin-Luther-University of Halle-Wittenberg (Germany). He is interested in 3D QSAR, molecular docking and molecular dynamics, and their applications in drug design and pharmacokinetics.

Didier Rognan leads the Drug Bioinformatics Group at the Laboratory for Molecular Pharmacochemistry in Illkirch (France). He is mainly interested in all aspects (method development, applications) of protein-based drug design and virtual screening.

Gerd Folkers is Professor of Pharmaceutical Chemistry at the ETH Zurich (Switzerland). The focus of his research is the molecular interation between drugs and their binding sites.