Computational Modeling of Biological Systems: From Molecules to Pathways

✍ Scribed by Yi Wang, J. Andrew McCammon (auth.), Nikolay V Dokholyan (eds.)

• Publisher: Springer-Verlag New York
• Year: 2012
• Tongue: English
• Leaves: 371
• Series: Biological and Medical Physics, Biomedical Engineering
• Edition: 1
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter....Pages i-vi
Front Matter....Pages 1-1
Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling....Pages 3-30
The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules....Pages 31-54
Discrete Molecular Dynamics Simulation of Biomolecules....Pages 55-73
Small Molecule Docking from Theoretical Structural Models....Pages 75-95
Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism....Pages 97-116
Quantum Mechanical Insights into Biological Processes at the Electronic Level....Pages 117-164
Front Matter....Pages 165-165
Multiscale Modeling of Virus Structure, Assembly, and Dynamics....Pages 167-189
Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model....Pages 191-214
The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases: Insights from Fully Atomistic Simulations....Pages 215-227
Front Matter....Pages 229-229
Computer Simulations of Mechano-Chemical Networks Choreographing Actin Dynamics in Cell Motility....Pages 231-256
Computational and Modeling Strategies for Cell Motility....Pages 257-296
Theoretical Analysis of Molecular Transport Across Membrane Channels and Nanopores....Pages 297-308
Front Matter....Pages 309-309
Modeling Protein Evolution....Pages 311-325
Modeling Structural and Genomic Constraints in the Evolution of Proteins....Pages 327-345
Modeling Proteins at the Interface of Structure, Evolution, and Population Genetics....Pages 347-361
Back Matter....Pages 363-364

✦ Subjects

Biophysics and Biological Physics;Molecular Medicine;Mathematical and Computational Biology;Computational Biology/Bioinformatics