Computational Modeling of Biological Systems: From Molecules to Pathways

Computational Modeling of Biological Systems: From Molecules to Pathways

by Nikolay V Dokholyan (Editor)


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Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

Product Details

ISBN-13: 9781461421450
Publisher: Springer New York
Publication date: 02/12/2012
Series: Biological and Medical Physics, Biomedical Engineering
Edition description: 2012
Pages: 366
Product dimensions: 6.10(w) x 9.25(h) x 0.04(d)

About the Author

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.

Table of Contents

Part I. Molecular Modeling.- Chapter 1. Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling.- Chapter 2. The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules.- Chapter 3. Discrete Molecular Dynamics Simulation of Biomolecules.- Chapter 4. Small Molecule Docking from Theoretical Structural Models.- Chapter 5. Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism.- Chapter 6. Quantum Mechanical Insights into Biological Processes at the Electronic Level.- Part II. Modeling Macromolecular Assemblies.- Chapter 7. Multiscale Modeling of Virus Structure, Assembly and Dynamics.- Chapter 8. Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model.- Chapter 9. The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases: Insights from Fully Atomistic Simulations.- Part III. Modeling Cells and Cellular Pathways.- Chapter 10. Computer Simulations of Mechano-Chemical Networks: Choreographing Actin Dynamics in Cell Motility.- Chapter 11. Computational and Modeling Strategies for Cell Motility.- Chapter 12. Theoretical Analysis of Molecular Transport Across Membrane Channels and Nanopores.- Part IV. Modeling Evolution.- Chapter 13. Modeling Protein Evolution.- Chapter 14. Modeling Structural and Genomic Constraints in the Evolution of Proteins.- Chapter 15. Modeling Proteins at the Interface of Structure, Evolution, and Population Genetics.

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