Computational Methods for Macromolecules: Challenges and Applications

Methods for Macromolecular Modeling (M3): Assessment of Progress and Future Perspectives.- I Biomolecular Dynamics Applications.- Mathematics and Molecular Neurobiology.- Structural and Dynamical Characterization of Nuclei Acid Water and Ion Binding Sites.- II Molecular Dynamics Methods.- A Test Set for Molecular Dynamics Algorithms.- Internal Coordinate Molecular Dynamics Based on the Spectroscopic B-Matrix.- The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure.- Overcoming Instabilities in Verlet-I/r-RESPA with the Mollified Impulse Method.- III Monte Carlo Methods.- On the Potential of Monte Carlo Methods for Simulating Macromolecular Assemblies.- Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique.- IV Other Conformational Sampling Methods.- Hierarchical Uncoupling-Coupling of Metastable Conformations.- Automatic Identification of Metastable Conformations via Self-Organized Neural Networks.- V Free Energy Methods.- Equilibrium and Non-Equilibrium Foundations of Free Energy Computational Methods.- Free-Energy Calculations in Protein Folding by Generahzed-Ensemble Algorithms.- Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions.- VI Long Range Interactions and Fast Electrostatics Methods.- Treecode Algorithms for Computing Nonbonded Particle Interactions.- A New Reciprocal Space Based Method for Treating Long Range Interactions in Ab Initio and Force-Field Based Calculations for Surfaces, Wires, and Clusters.- Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking.- VII Statistical Approaches to Protein Structures.- FoldRecognition Using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model.- Identification of Sequence-Specific Tertiary Packing Motifs in Protein Structures using Delaunay

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REVIEW BY ANDRZEJ KLOCZKOWSKI, BAKER CENTER FOR BIOINFORMATICS AND BIOLOGICAL STATISTICS, IOWA STATE UNIVERSITY

"The authors of the articles in the book are the top specialists in their fields and the book presents the current state of the art for the broad spectrum of all currently used methods and techniques of macromolecular modeling. The book might be very useful for all readers interested in the computational modeling of macromolecules. Several articles in the book cover different aspects of protein modeling, so I would highly recommend this book to all readers interested in modeling of proteins."