Computational Modeling of Biological Systems

From Molecules to Pathways

Editors:

ISBN: 978-1-4614-2145-0 (Print) 978-1-4614-2146-7 (Online)

Table of contents (15 chapters)

  1. Front Matter

    Pages i-vi

  2. Molecular Modeling

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Chapter

      Pages 3-30

      Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling

    3. No Access

      Book Chapter

      Pages 31-54

      The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules

    4. No Access

      Book Chapter

      Pages 55-73

      Discrete Molecular Dynamics Simulation of Biomolecules

    5. No Access

      Book Chapter

      Pages 75-95

      Small Molecule Docking from Theoretical Structural Models

    6. No Access

      Book Chapter

      Pages 97-116

      Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism

    7. No Access

      Book Chapter

      Pages 117-164

      Quantum Mechanical Insights into Biological Processes at the Electronic Level

  3. Modeling Macromolecular Assemblies

    1. Front Matter

      Pages 165-165

    2. No Access

      Book Chapter

      Pages 167-189

      Multiscale Modeling of Virus Structure, Assembly, and Dynamics

    3. No Access

      Book Chapter

      Pages 191-214

      Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model

    4. No Access

      Book Chapter

      Pages 215-227

      The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases: Insights from Fully Atomistic Simulations

  4. Modeling Cells and Cellular Pathways

    1. Front Matter

      Pages 229-229

    2. No Access

      Book Chapter

      Pages 231-256

      Computer Simulations of Mechano-Chemical Networks Choreographing Actin Dynamics in Cell Motility

    3. No Access

      Book Chapter

      Pages 257-296

      Computational and Modeling Strategies for Cell Motility

    4. No Access

      Book Chapter

      Pages 297-308

      Theoretical Analysis of Molecular Transport Across Membrane Channels and Nanopores

  5. Modeling Evolution

    1. Front Matter

      Pages 309-309

    2. No Access

      Book Chapter

      Pages 311-325

      Modeling Protein Evolution

    3. No Access

      Book Chapter

      Pages 327-345

      Modeling Structural and Genomic Constraints in the Evolution of Proteins

    4. No Access

      Book Chapter

      Pages 347-361

      Modeling Proteins at the Interface of Structure, Evolution, and Population Genetics

  6. Back Matter

    Pages 363-364