Molecular Modeling and Prediction of Bioactivity

Table of Contents

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   Book Overview
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   Chapter 1 Strategies for Molecular Design Beyond the Millennium
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   Chapter 2 Multivariate Design and Modelling in QSAR, Combinatorial Chemistry, and Bioinformatics
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   Chapter 3 QSAR Study of PAH Carcinogenic Activities: Test of a General Model for Molecular Similarity Analysis
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   Chapter 4 Comparative Molecular Field Analysis of Aminopyridazine Acetylcholinesterase Inhibitors
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   Chapter 5 The Influence of Structure Representation on QSAR Modelling
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   Chapter 6 The Constrained Principal Property (CPP) Space in QSAR — Directional and Non-Directional Modelling Approaches
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   Chapter 7 Handling Information from 3D Grid Maps for QSAR Studies
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   Chapter 8 Gaussian-Based Approaches to Protein-Structure Similarity
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    Chapter 9 Molecular Field-Derived Descriptors for the Multivariate Modeling of Pharmacokinetic Data
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    Chapter 10 Validating Novel QSAR Descriptors for Use in Diversity Analysis
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    Chapter 11 Structural and Energetic Aspects of Protein-Ligand Binding in Drug Design
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    Chapter 12 Use of MD-Derived Shape Descriptors as a Novel Way to Predict the in Vivo Activity of Flexible Molecules
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    Chapter 13 A View on Affinity and Selectivity of Nonpeptidic Matrix Metalloproteinase Inhibitors from the Perspective of Ligands and Target
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    Chapter 14 On the Use of SCRF Methods in Drug Design Studies
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    Chapter 15 3D-QSAR Study of 1,4-Dihydropyridines Reveals Distinct Molecular Requirements of Their Binding Site in the Resting and the Inactivated State of Voltage-Gated Calcium Channels
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    Chapter 16 Pharmacophore Development for the Interaction of Cytochrome P450 1A2 with Its Substrates and Inhibitors
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    Chapter 17 Analysis of a Large, High-Throughput Screening Data Using Recursive Partitioning
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    Chapter 18 3D Structure Descriptors for Biological Activity
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    Chapter 19 Fragment-Based Screening of Ligand Databases
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    Chapter 20 The Computer Simulation of High Throughput Screening of Bioactive Molecules
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    Chapter 21 5-HT 1A Receptors Mapping by Conformational Analysis (2D NOESY/MM) and “Three Way Modelling” (HASL, CoMFA, PARM)
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    Chapter 22 Design and Activity Estimation of a New Class of Analgesics
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    Chapter 23 Unified Pharmacophoric Model for Cannabinoids and Aminoalkylindoles
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    Chapter 24 Chemometric Detection of Binding Sites of 7TM Receptors
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    Chapter 25 Specmat: Spectra as Molecular Descriptors for the Prediction of Biological Activity
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    Chapter 26 Hydrogen Bond Contributions to Properties and Activities of Chemicals and Drugs
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    Chapter 27 Predicting Peptide Absorption
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    Chapter 28 Physicochemical High Throughput Screening (pC-HTS): Determination of Membrane Permeability, Partitioning and Solubility
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    Chapter 29 Understanding and Estimating Membrane/Water Partition Coefficients: Approaches to Derive Quantitative Structure Property Relationships
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    Chapter 30 Prediction of Human Intestinal Absorption of Drug Compounds from Molecular Structure
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    Chapter 31 Free-Wilson-Type QSAR Analyses Using Linear and Nonlinear Regression Techniques
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    Chapter 32 QSAR Studies of Picrodendrins and Related Terpenoids — Structural Differences Between Antagonist Binding Sites on GABA Receptors of Insects and Mammals
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    Chapter 33 Molecular lipophilicity descriptors: a multivariate analysis
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    Chapter 34 World Wide Web-Based Calculation of Substituent Parameters for QSAR Studies
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    Chapter 35 Combine and Free-Wilson QSAR Analysis of Nuclear Receptor-DNA Binding
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    Chapter 36 QSAR Model Validation
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    Chapter 37 QSPR Prediction of Henry’s Law Constant: Improved Correlation with New Parameters
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    Chapter 38 QSAR of a Series of Carnitine Acetyl Transferase (CAT) Substrates
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    Chapter 39 “Classical” and Quantum Mechanical Descriptors for Phenolic Inhibition of Bacterial Growth
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    Chapter 40 Hydrogen Bond Acceptor and Donor Factors, C a and C d : New QSAR Descriptors
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    Chapter 41 Development and Validation of a Novel Variable Selection Technique with Application to QSAR Studies
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    Chapter 42 Qsar Studies of Environmental Estrogens
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    Chapter 43 Quantitative Structure-Activity Relationship of Antimutagenic Benzalacetones and Related Compounds
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    Chapter 44 Multivariate Regression Excels Neural Networks, Genetic Algorithm and Partial Least-Squaresin Qsar Modeling
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    Chapter 45 Structure — Activity Relationships of Nitrofuran Derivatives with Antibacterial Activity
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    Chapter 46 QSAR Approach for the Selection of Congeneric Compounds with Similar Toxicological Modes of Action
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    Chapter 47 Strategies for Selection of Test Compounds in Structure-Affinity Modelling of Active Carbon Adsorption Performance: A Multivariate Approach
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    Chapter 48 Design and QSAR of Dihydropyrazolo[4,3-c]Quinolinones as PDE4 Inhibitors
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    Chapter 49 QSAR Based on Biological Microcalorimetry
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    Chapter 50 Cinnoline Analogs of Quinolones: Structural Consequences of the N Atom Introduction in the Position 2
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    Chapter 51 Joint Continuum Regression for Analysis of Multiple Responses
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    Chapter 52 Putative Pharmacophores for Flexible Pyrethroid Insecticides
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    Chapter 53 Predicting Maximum Bioactivity of Dihydrofolate Reductase Inhibitors
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    Chapter 54 Evaluation of Carcinogenicity of the Elements by Using Nonlinear Mapping
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    Chapter 55 Partition Coefficients of Binary Mixtures of Chemicals: Possibility for the QSAR Analysis
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    Chapter 56 A CoMFA study on antileishmaniasis bisamidines
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    Chapter 57 Antileishmanial Chalcones: Statistical Design and 3D-QSAR Analysis
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    Chapter 58 Chemical Function Based Alignment Generation for 3D QSAR of Highly Flexible Platelet Aggregation Inhibitors
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    Chapter 59 3D QSAR on Mutagenic Heterocyclic Amines That are Substrates of Cytochrome P450 1A2
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    Chapter 60 Application of 4D-QSAR Analysis to a Set of Prostaglandin, PGF 2 α, Analogs
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    Chapter 61 Determination of the Cholecalciferol-Lipidcomplex Using a Combination of Comparative Modelling and NMR Spectroscopy
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    Chapter 62 Comparative Binding Energy (Combine) Analysis on a Series of Glycogen Phosphorylase Inhibitors. Comparison with Grid/Golpe Models
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    Chapter 63 Molecular Modeling and Prediction of Bioactivity
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    Chapter 64 3D-QSAR, GRID Descriptors and Chemometric Tools in the Development of Selective Antagonists of Muscarinic Receptor
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    Chapter 65 Small Cyclic Peptide Sar Study Using Apex-3D System: Somatostatin Receptor Type 2 ( SSTR2 ) Specific Pharmacophores
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    Chapter 66 3D Quantitative Structure-Activity Relationship (COMFA) Study of Heterocyclic Arylpiperazine Derivatives with 5-HT 1A Activity
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    Chapter 67 Molecular Similarity Analysis and 3D-QSAR of Neonicotinoid Insecticides
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    Chapter 68 3D-SAR Studies on a Series of Sulfonate Dyes as Protection Agents Against β-Amyloid Induced in Vitro Neurotoxicity
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    Chapter 69 A New Molecular Structure Representation: Spectral Weighted Molecular (SWM) Signals and Spectral Weighted Invariant Molecular (SWIM) Descriptors
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    Chapter 70 3D QSAR of Prolyl 4-Hydroxylase Inhibitors
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    Chapter 71 Aromatase Inhibitors: Comparison between a CoMFA Model and the Enzyme Active Site
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    Chapter 72 Imidazoline Receptor Ligands — Molecular Modeling and 3D-QSAR CoMFA
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    Chapter 73 Reversible Inhibition of MAO-A and B by Diazoheterocyclic Compounds: Development of QSAR/CoMFA Models
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    Chapter 74 Modelling of the 5-HT 2A Receptor and Its Ligand Complexes
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    Chapter 75 Towards the Understanding of Species Selectivity and Resistance of Antimalarial DHFR Inhibitors
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    Chapter 76 Modeling of Suramin-TNFα Interactions
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    Chapter 77 De Novo Design of Inhibitors of Protein Tyrosine Kinase pp60 c-src
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    Chapter 78 Elucidation of Active Conformations of Drugs Using Conformer Sampling by Molecular Dynamics Calculations and Molecular Overlay
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    Chapter 79 Differences in Agonist Binding Pattern for the GABA A and the AMPA Receptors Illustrated by High-Level AB Initio Calculations
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    Chapter 80 Stabilization of the Ammonium-Carboxylate Ion-Pair by an Aromatic Ring
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    Chapter 81 Structural Requirements for Binding to Cannabinoid Receptors
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    Chapter 82 Design, Synthesis and Testing of Novel Inhibitors of Cell Adhesion
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    Chapter 83 Conformational Analysis and Pharmacophore Identification of Potential Drugs for Osteoporosis
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    Chapter 84 Molecular Modelling of DNA Adducts of BBR3464: A New Phase I Clinical Agent
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    Chapter 85 Prediction of Activity for a Set of Flavonoids Against HIV-1 Integrase
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    Chapter 86 Structure-Based Discovery of Inhibitors of an Essential Purine Salvage Enzyme in Tritrichomonas Foetus
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    Chapter 87 A 3D-Pharmacophore Model for Dopamine D 4 Receptor Antagonists
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    Chapter 88 Molecular Modeling and Structure-Based Design of Direct Calcineurin Inhibitors
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    Chapter 89 Conformational Flexibility and Receptor Interaction
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    Chapter 90 Investigating the Mimetic Potential of β-Turn Mimetics
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    Chapter 91 Conformational Aspects of the Interaction of New 2,4-Dihydroxyacetophenone Derivatives with Leukotriene Receptors
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    Chapter 92 Conformational Studies of Poly(Methylidene Malonate 2.1.2)
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    Chapter 93 A Peptidic Binding Site Model for PDE 4 Inhibitors
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    Chapter 94 Molecular Dynamics Simulations of the Binding of a GnRH Agonist to a Model GnRH Receptor
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    Chapter 95 Analysis of Affinities of Penicillins for a Class C β-Lactamase by Molecular Dynamics Simulations
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    Chapter 96 Theoretical Approaches for Rational Design of Proteins
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    Chapter 97 Amisulpride, Sultopride and Sulpiride: Comparison of Conformational and Physico-Chemical Properties
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    Chapter 98 Entropic Trapping: Its Possible Role in Biochemical Systems
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     Chapter 99 Structural Requirements to Obtain Potent CAXX Mimic P21-Ras-Farnesyltransferase Inhibitors
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     Chapter 100 Hydrogen-Bonding Hotspots as an Aid for Site-Directed Drug Design
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     Chapter 101 Superposition of Flexible Ligands to Predict Positions of Receptor Hydrogen-Bonding Atoms
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     Chapter 102 Comparative Molecular Field Analysis of Multidrug Resistance Modifiers
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     Chapter 103 Pharmacophore Model of Endothelin Antagonists
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     Chapter 104 The Electron-Topological Method (ETM): Its Further Development and Use in the Problems of SAR Study
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     Chapter 105 Moldivs — A New Program for Molecular Similarity and Diversity Calculations
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     Chapter 106 Easy Does It: Reducing Complexity in Ligand-Protein Docking
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     Chapter 107 Study of the Molecular Similarity among Three HIV Reverse Transcriptase Inhibitors in Order to Validate GAGS, a Genetic Algorithm for Graph Similarity Search
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     Chapter 108 A Decision Tree Learning Approach for the Classification and Analysis of High-Throughput Screening Data
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     Chapter 109 Application of PARM to Constructing and Comparing 5-HT 1A and α 1 Receptor Models
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     Chapter 110 A Novel Computational Method for Predicting the Transmembranal Structure of G-Protein Coupled Anaphylatoxin Receptors, C5aR and C3aR
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     Chapter 111 Receptor-Based Molecular Diversity: Analysis of HIV Protease Inhibitors
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     Chapter 112 Application of Self-Organizing Neural Networks with Active Neurons for QSAR Studies
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     Chapter 113 Application of Artificial Neural Networks in QSAR of a New Model of Phenylpiperazine Derivatives 1 with Affinity for 5-HT 1A and α l Receptors: A Comparision of ANN Models
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     Chapter 114 Atypical Antipsychotics: Modelling and QSAR
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     Chapter 115 Genetic Algorithms: Results too Good to be True?
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     Chapter 116 Property Patches in GPCRs: A Multivariate Study
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     Chapter 117 A Stochastic Method for the Positioning of Protons in X-ray Structures of Biomolecules
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     Chapter 118 Molecular Field Topology Analysis (MFTA) as the Basis for Molecular Design
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     Chapter 119 Rank Distance Clustering — A New Method for the Analysis of Embedded Activity Data
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     Chapter 120 The Application of Machine Learning Algorithms to Detect Chemical Properties Responsible for Carcinogenicity
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     Chapter 121 Study of Geometrical/Electronic Structures — Carcinogenic Potency Relationship with Counterpropagation Neural Networks
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     Chapter 122 Combining Molecular Modelling with the Use of Artificial Neural Networks as an Approach to Predicting Substituent Constants and Bioactivity
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     Chapter 123 Application of Neural Networks for Estimating Partition Coefficient Based on Atom-Type Electrotopological State Indices
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     Chapter 124 Variable Selection in the Cascade-Correlation Learning Architecture
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     Chapter 125 Chemical Fingerprints Containing Biological and Other Nonstructural Data
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     Chapter 126 Rodent Tumor Profiles Induced by 536 Chemicals Carcinogens: An Information Intensive Analysis
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     Chapter 127 Comparison of Several Ligands for the 5-HT 1D Receptor Using the Kohonen Self-Organizing-Maps Technique
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     Chapter 128 Binding Energy Studies on the Interaction between Berenil Derivatives and Thrombin and the B-DNA Dodecamer D(CGCGAATTCGCG) 2
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     Chapter 129 A Comparison of AB Initio , Semi-Empirical, and Molecular Mechanics Approaches to Compute Molecular Geometries and Electrostatic Descriptors of Heteroatomic Ring Fragments Observed in Drugs Molecules
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     Chapter 130 Elaboration of an Interaction Model Between Zolpidem and the ω 1 Modulatory Site of GABA A Receptor Using Site-Directed Mutagenesis
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     Chapter 131 SLIPPER — A New Program for Water Solubility, Lipophilicity and Permeability Prediction
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     Chapter 132 Correlation of Intestinal Drug Permeability in Humans ( In Vivo ) with Experimentally and Theoretically Derived Parameters
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     Chapter 133 A Critical Appraisal of logP Calculation Procedures Using Experimental Octanol-Water and Cyclohexane-Water Partition Coefficients and HPLC Capacity Factors for a Series of Indole Containing Derivatives of 1,3,4-Thiadiazole and 1,2,4-Triazole
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     Chapter 134 Determination of Accurate Thermodynamics of Binding for Proteinase-Inhibitor Interactions