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G protein coupled receptors : modeling, activation, interactions and virtual screening.

Author: P Michael Conn
Publisher: Burlington : Elsevier Science, 2013.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
<Ul> <ul> This new volume of <i>Methods in Enzymology</i> continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers G protein coupled receptors, and includes chapters on such topics as GPCR modelling, interactions with other molecules, virtual screening and GPCR activation. </ul></ul><br><br><ul>  Read more...
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Genre/Form: Electronic books
Additional Physical Format: Print version:
Conn, P. Michael.
G Protein Coupled Receptors : Modeling, Activation, Interactions and Virtual Screening.
Burlington : Elsevier Science, ©2013
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: P Michael Conn
ISBN: 9780124079441 012407944X
OCLC Number: 830163808
Description: 1 online resource (541 pages)
Contents: Front Cover ; G Protein Coupled Receptors: Modeling, Activation, Interactions and Virtual Screening; Copyright; Contents; Contributors; Preface; Methods in Enzymology; Chapter One: The Protein Local Optimization Program and G-Protein-Coupled Receptors: Loop Restoration and Applications to ...; 1. Introduction; 2. PLOP Performance for Loop Prediction; 3. PLOP and GPCRs; 4. Loop Prediction with the Single-Residue Library; 4.1. Single-loop prediction; 4.1.1. The buildup stage; 4.1.2. The closure stage; 4.1.3. The clustering stage; 4.1.4. Optimization and scoring stage; 4.2. Full-loop prediction. 4.2.1. Initial stage (Init)4.2.2. First constrained refinement stage (Ref1); 4.2.3. The fixed stages (Fix1, Fix2,, Fixn); 4.2.4. Second constrained refinement stage; 5. Loop Prediction with the Dipeptide Library; 6. Hierarchical Loop Prediction with Surrounding Side Chain Optimization; 6.1. Removal of side chains during backbone sampling; 6.2. Simultaneous optimization of side chains in both loop and nearby regions; 7. Additional Sampling Methods; 7.1. Prediction of loops containing small helical secondary structure; 7.2. Phase space partitioning method. 8. VSGB 2.0: The Newest Energy Model Incorporated into PLOP8.1. Hydrogen bonding correction (EHB); 8.2. Self-contact correction; 8.3. <U+0073>-<U+0073> packing correction; 8.4. Hydrophobic term; 9. Conclusions; Acknowledgments; References; Chapter Two: Modeling Active GPCR Conformations; 1. Introduction; 2. General Approaches; 2.1. Homology modeling; 2.2. De novo methods; 3. Agonist-Induced Activation; 4. Simulation Methods; 4.1. The activation pathway; 4.2. Protonation; 4.3. Parameters; 4.4. Oligomerization and activation; 5. Microswitches; 5.1. DRY and the ionic lock; 5.2. The rotamer toggle switch. 5.3. EL26. Biophysical Restraints; 7. Virtual Screening; 8. Class B GPCRs; Acknowledgments; References; Chapter Three: Molecular Modeling of Adenosine Receptors; 1. Introduction; 2. Adenosine A2a Receptor; 2.1. X-ray structures; 2.2. Receptor activation; 3. Receptor Modeling; 3.1. Building adenosine receptor models; 3.2. Homology modeling; 3.2.1. Alignment; 3.2.2. Modeling; 3.2.3. Detailed procedure of the alignment and modeling steps; 3.2.4. Optimization; 3.2.5. Detailed procedure of the optimization step; 3.3. MM/PBSA; 3.4. Validation methods; 3.5. Receptor oligomerization. 3.5.1. Adenosine receptor homo- and heterooligomerization3.5.2. Procedure for modeling an AA2AR dimer; 4. Summary; References; Chapter Four: Predicting G-Protein-Coupled Receptors Families Using Different Physiochemical Properties and Pseudo Amino ...; 1. Introduction; 1.1. G-protein-coupled receptors; 1.2. Pharmacological and phylogenetic classification of GPCRs; 1.3. Classification by alignment-independent classifiers; 2. GPCRs Prediction; 2.1. Feature extraction strategies; 2.1.1. Amphiphilic Pseudo amino acid composition; 2.1.2. Wavelet-based MSE.

Abstract:

<Ul> <ul> This new volume of <i>Methods in Enzymology</i> continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers G protein coupled receptors, and includes chapters on such topics as GPCR modelling, interactions with other molecules, virtual screening and GPCR activation. </ul></ul><br><br><ul> <ul></ul><li>Continues the legacy of this premier serial with quality chapters authored by leaders in the field </li><li>Covers G protein coupled receptors </li><li>Contains chapters on such topics as GPCR modelling, interactions with other.

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