Computational Methods for Macromolecules: Challenges and Applications

Chapter 1 Methods for Macromolecular Modeling (M 3 ): Assessment of Progress and Future Perspectives

Chapter 2 Mathematics and Molecular Neurobiology

Chapter 3 Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites

Chapter 4 A Test Set for Molecular Dynamics Algorithms

Chapter 5 Internal Coordinate Molecular Dynamics Based on the Spectroscopic B-Matrix

Chapter 6 The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure

Chapter 7 Overcoming Instabilities in Verlet-I/r-RESPA with the Mollified Impulse Method

Chapter 8 On the Potential of Monte Carlo Methods for Simulating Macromolecular Assemblies

Chapter 9 Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique

Chapter 10 Hierarchical Uncoupling-Coupling of Metastable Conformations

Chapter 11 Automatic Identification of Metastable Conformations via Self-Organized Neural Networks

Chapter 12 Equilibrium and Nonequilibrium Foundations of Free Energy Computational Methods

Chapter 13 Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms

Chapter 14 Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions

Chapter 15 Treecode Algorithms for Computing Nonbonded Particle Interactions

Chapter 16 A New Reciprocal Space Based Method for Treating Long Range Interactions in Ab Initio and Force-Field Based Calculations for Surfaces, Wires, and Clusters

Chapter 17 Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking

Chapter 18 Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model

Chapter 19 Identification of Sequence-Specific Tertiary Packing Motifs in Protein Structures using Delaunay Tessellation