Computational Modeling of Biological Systems

1. Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling
Yi Wang, J. Andrew McCammon

2. The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules
Jeffrey K. Noel, José N. Onuchic

3. Discrete Molecular Dynamics Simulation of Biomolecules
Feng Ding, Nikolay V. Dokholyan

4. Small Molecule Docking from Theoretical Structural Models
Eva Maria Novoa, Lluis Ribas Pouplana, Modesto Orozco

5. Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism
Srinivas Ramachandran, Nikolay V. Dokholyan

6. Quantum Mechanical Insights into Biological Processes at the Electronic Level
Anastassia N. Alexandrova

7. Multiscale Modeling of Virus Structure, Assembly, and Dynamics
Eric R. May, Karunesh Arora, Ranjan V. Mannige, Hung D. Nguyen, Charles L. Brooks

8. Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model
Andrea Magno, Riccardo Pellarin, Amedeo Caflisch

9. The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases: Insights from Fully Atomistic Simulations
Chun Wu, Joan-Emma Shea

10. Computer Simulations of Mechano-Chemical Networks Choreographing Actin Dynamics in Cell Motility
Pavel I. Zhuravlev, Longhua Hu, Garegin A. Papoian

11. Computational and Modeling Strategies for Cell Motility
Qi Wang, Xiaofeng Yang, David Adalsteinsson, Timothy C. Elston, Ken Jacobson, Maryna Kapustina, M. Gregory Forest

12. Theoretical Analysis of Molecular Transport Across Membrane Channels and Nanopores
Anatoly B. Kolomeisky

13. Modeling Protein Evolution
Richard Goldstein, David Pollock

14. Modeling Structural and Genomic Constraints in the Evolution of Proteins
Ugo Bastolla, Markus Porto

15. Modeling Proteins at the Interface of Structure, Evolution, and Population Genetics
Ashley I. Teufel, Johan A. Grahnen, David A. Liberles

Keywords: Physics, Biophysics and Biological Physics, Molecular Medicine, Mathematical and Computational Biology, Computational Biology/Bioinformatics