Computational Modeling of Biological Systems (eBook)

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.

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.