Computational Modeling of Biological Systems, 2012
From Molecules to Pathways
Biological and Medical Physics, Biomedical Engineering Series

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.

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

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.

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