Book Volume 443 2008

Molecular Modeling of Proteins

Editors:

ISBN: 978-1-58829-864-5 (Print) 978-1-59745-177-2 (Online)

Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi

  2. Methodology

    1. No Access

      Protocol

      Pages 3-23

      Molecular Dynamics Simulations

    2. No Access

      Protocol

      Pages 25-36

      Monte Carlo Simulations

    3. No Access

      Protocol

      Pages 37-62

      Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes

    4. No Access

      Protocol

      Pages 63-88

      Comparison of Protein Force Fields for Molecular Dynamics Simulations

    5. No Access

      Protocol

      Pages 89-106

      Normal Modes and Essential Dynamics

  3. Free Energy Calculations

    1. No Access

      Protocol

      Pages 109-120

      Calculation of Absolute Protein–Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method

    2. No Access

      Protocol

      Pages 121-144

      Free Energy Calculations Applied to Membrane Proteins

  4. Molecular Modeling of Membrane Proteins

    1. No Access

      Protocol

      Pages 147-160

      Molecular Dynamics Simulations of Membrane Proteins

    2. No Access

      Protocol

      Pages 161-179

      Membrane-Associated Proteins and Peptides

    3. No Access

      Protocol

      Pages 181-196

      Implicit Membrane Models for Membrane Protein Simulation

  5. Protein Structure Determination

    1. No Access

      Protocol

      Pages 199-212

      Comparative Modeling of Proteins

    2. No Access

      Protocol

      Pages 213-227

      Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints

    3. No Access

      Protocol

      Pages 229-255

      Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

  6. Conformational Change

    1. No Access

      Protocol

      Pages 258-275

      Conformational Changes in Protein Function

    2. No Access

      Protocol

      Pages 277-295

      Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations

    3. No Access

      Protocol

      Pages 297-330

      Modeling of Protein Misfolding in Disease

  7. Applications to Drug Design

    1. No Access

      Protocol

      Pages 333-351

      Identifying Putative Drug Targets and Potential Drug Leads

    2. No Access

      Protocol

      Pages 353-364

      Receptor Flexibility for Large-Scale In Silico Ligand Screens

    3. No Access

      Protocol

      Pages 365-382

      Molecular Docking

  8. Back Matter

    Pages 383-390