Computational Methods for Macromolecules: Challenges and Applications: Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, October 12–14, 2000(24 Lecture Notes in Computational Science and Engineering)

This special volume collects invited articles by participants of the Third International Workshop on Methods for Macromolecular Modeling, Courant Institute of Mathematical Sciences, Oct. 12-14, 2000. Leading developers of methods for biomolecular simulations review advances in Monte Carlo and molecular dynamics methods, free energy computational methods, fast electrostatics (particle-mesh Ewald and fast multipole methods), mathematics, and molecular neurobiology, nucleic acid simulations, enzyme reactions, and other essential applications in biomolecular simulations. A Perspectives article by the editors assesses the directions and impact of macromolecular modeling research, including genomics and proteomics. These reviews and original papers by applied mathematicians, theoretical chemists, biomedical researchers, and physicists are of interest to interdisciplinary research students, developers and users of biomolecular methods in academia and industry.

Table of Contents:
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 Tessellation.- Appendix: Color Plates.

Review :
POLYMER NEWS 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."