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Computational Modeling of Biological Systems

From Molecules to Pathways

  • Book
  • © 2012

Overview

Editors:
  1. Nikolay V Dokholyan

    1. , Biochemistry and Biophysics, University of North Carolina at Chapel H, Chapel Hill, USA

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  • Reviews established modeling approaches of biological systems across multiple length and time scales from molecules to cells
  • Covers recent and emerging computational techniques in modelling biological systems
  • Provides a fresh outlook on the topic by covering multiscale modelling and includes a section on molecular evolution
  • Can be used as a guide for selecting methods for studying biological systems
  • Includes supplementary material: sn.pub/extras

Part of the book series: Biological and Medical Physics, Biomedical Engineering (BIOMEDICAL)

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Table of contents (15 chapters)

  1. Front Matter

    Pages i-vi
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  2. Molecular Modeling

    1. Front Matter

      Pages 1-1
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    2. Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling

      • Yi Wang, J. Andrew McCammon
      Pages 3-30

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

      • Jeffrey K. Noel, José N. Onuchic
      Pages 31-54

    4. Discrete Molecular Dynamics Simulation of Biomolecules

      • Feng Ding, Nikolay V. Dokholyan
      Pages 55-73

    5. Small Molecule Docking from Theoretical Structural Models

      • Eva Maria Novoa, Lluis Ribas de Pouplana, Modesto Orozco
      Pages 75-95

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

      • Srinivas Ramachandran, Nikolay V. Dokholyan
      Pages 97-116

    7. Quantum Mechanical Insights into Biological Processes at the Electronic Level

      • Anastassia N. Alexandrova
      Pages 117-164

  3. Modeling Macromolecular Assemblies

    1. Front Matter

      Pages 165-165
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    2. Multiscale Modeling of Virus Structure, Assembly, and Dynamics

      • Eric R. May, Karunesh Arora, Ranjan V. Mannige, Hung D. Nguyen, Charles L. Brooks III
      Pages 167-189

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

      • Andrea Magno, Riccardo Pellarin, Amedeo Caflisch
      Pages 191-214

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

      • Chun Wu, Joan-Emma Shea
      Pages 215-227

  4. Modeling Cells and Cellular Pathways

    1. Front Matter

      Pages 229-229
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    2. Computer Simulations of Mechano-Chemical Networks Choreographing Actin Dynamics in Cell Motility

      • Pavel I. Zhuravlev, Longhua Hu, Garegin A. Papoian
      Pages 231-256

    3. Computational and Modeling Strategies for Cell Motility

      • Qi Wang, Xiaofeng Yang, David Adalsteinsson, Timothy C. Elston, Ken Jacobson, Maryna Kapustina et al.
      Pages 257-296

    4. Theoretical Analysis of Molecular Transport Across Membrane Channels and Nanopores

      • Anatoly B. Kolomeisky
      Pages 297-308

  5. Modeling Evolution

    1. Front Matter

      Pages 309-309
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    2. Modeling Protein Evolution

      • Richard Goldstein, David Pollock
      Pages 311-325

    3. Modeling Structural and Genomic Constraints in the Evolution of Proteins

      • Ugo Bastolla, Markus Porto
      Pages 327-345

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

      • Ashley I. Teufel, Johan A. Grahnen, David A. Liberles
      Pages 347-361
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Keywords

About this book

Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Editors and Affiliations

  • , Biochemistry and Biophysics, University of North Carolina at Chapel H, Chapel Hill, USA

    Nikolay V Dokholyan

About the editor

Dr. Nikolay Dokholyan joined the Department of Biochemistry and Biophysics in the University of North Carolina at Chapel Hill, School of Medicine as an Assistant Professor. In 2008, Dr. Dokholyan was promoted as Associate Professor. Dr. Dokholyan is currently the Director of the Center for Computational and Systems Biology and the Graduate Director of the Program in Molecular and Cellular Biophysics at UNC.

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