Frontiers in computational chemistry. Volume 3 / edited by Dr. Zaheer Ul-Haq & Dr. Jeffry D. Madura.

Print version record.

Includes bibliographical references and index.

PREFACE ; List of Contributors ; In Silico Approaches for Drug Discovery and Development ; 1. INTRODUCTION; 2. COMPUTER AIDED DRUG DESIGN STRATEGIES; 2.1. Ligand Based Drug Discovery; 2.2. Structure Based Drug Discovery; 3. TOPICS IN CADD; 3.1. Databases; 3.1.1. Small Molecule Databases; 3.1.2. Preparation of Ligand Libraries; 3.1.3. Virtual Combinatorial libraries; 3.1.4. Representation of Small Molecules; 3.1.5. Molecular Descriptors/Features; 3.2. Target Databases for Computer-Aided Drug Design; 3.3. Similarity Searches; 3.4. Quantitative Structure-Activity Relationship (QSAR).

3.4.1. Classical QSAR (1D/2D)3.4.2. 3D-QSAR; 3.4.3. Multidimensional QSAR; 3.5. Pharmacophores; 3.6. Comparative Modeling; 3.7. Binding Site Detection and Characterization; 3.8. Protein -- Ligand Docking; 3.8.1. Molecular Docking Methods; 3.8.2. Protein Flexibility in Docking; 4. MOLECULAR DYNAMICS SIMULATIONS IN DRUG DISCOVERY AND DESIGN; 4.1. MD Simulations; 4.2. Refinement of Homology Models; 4.3. Combining Docking and MD Simulations; 4.3.1. Receptor Conformation (Preparation of Receptor Structure); 4.3.2. Ensemble Generation; 4.3.3. Refinement of Docked Complexes.

4.4. Free Energy Calculations5. ASSESSMENT OF ABSORPTION DISTRIBUTION METABOLISM EXCRETION AND TOXICITY PROPERTIES; 5.1. Drug Attrition in the Drug Development Phase; 5.2. Compound Library Filters; 5.3. Drug Metabolism: Cytochrome P450; 5.4. Prediction of Human Ether-A-Go-Go Related Gene Binding; 6. PROTEIN -- PROTEIN INTERACTIONS AS DRUG TRAGETS; 6.1. Peptide and Peptidomimetics as ppi Inhibitors; CONFLICT OF INTEREST; ACKNOWLEDGEMENTS; REFERENCES; Computational Chemistry Assisted Design and Screening of Ligand-Solvent Systems for Metal Ion Separation ; 1. INTRODUCTION.

2. COMPUTATIONAL METHODOLOGY2.1. Moller-Plesset Perturbation Theory; 2.2. Couple Cluster Method; 2.3. Density Functional Theory (DFT); 2.4. Local Density Approximation; 2.5. Generalized Gradient Approximation; 2.6. Conductor Like Screening Model (COSMO); 2.7. Basis Set Superposition Error (BSSE); 2.8. Present Approach of Design and Evaluation; 2.8.1. Evaluation of Structural Parameters; 2.8.2. Evaluation of Interaction Parameters; 2.8.3. Evaluation of Thermodynamic Parameters; 2.8.4. Calculation of Separation Parameters ; 3. STRUCTURES AND STRCTURAL PARAMETERS.

3.1. Microsolvation of Metal Ions3.2. Coordination Number and Radial Distribution Function; 3.3. Macrocyclic Crown Ethers; 3.4. Cavity Size of the Host Crown Ethers; 3.5. Tuned Extended Crown Ethers; 3.6. Conformation; 3.7. Donors; 3.8. Calix-Crown Ethers; 3.9. Organophosphorus Ligands; 3.10. Diglycolamide Ligands; 3.11. Carbon Nanotube Functionalized Diglycolamic Acids; 3.12. Ionic Liquids; 4. INTERACTION PARAMETERS -BINDING ENEGY; 4.1. Cavity Dependence ; 4.2. Conformer Dependence; 4.3. Donor Atom Dependence; 4.4. Binding Interaction towards Calix-Crown Ethers.

4.5. Binding Interaction with Organophosphorous Ligands.

Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. The third volume of this series features four chapters covering in silico approaches to computer aided drug design, modeling of platinum and adjuvant anti-cancer drugs, allostery in proteins and studies on the theory of chemical space in electron systems.

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