Ebook: Computational Methods for Macromolecules: Challenges and Applications: Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, October 12–14, 2000

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."

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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.

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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.
Content:
Front Matter....Pages I-IX
Front Matter....Pages 1-1
Methods for Macromolecular Modeling (M3): Assessment of Progress and Future Perspectives....Pages 3-27
Front Matter....Pages 29-29
Mathematics and Molecular Neurobiology....Pages 31-60
Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites....Pages 61-70
Front Matter....Pages 71-71
A Test Set for Molecular Dynamics Algorithms....Pages 73-103
Internal Coordinate Molecular Dynamics Based on the Spectroscopic B-Matrix....Pages 104-128
The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure....Pages 129-145
Overcoming Instabilities in Verlet-I/r-RESPA with the Mollified Impulse Method....Pages 146-174
Front Matter....Pages 175-175
On the Potential of Monte Carlo Methods for Simulating Macromolecular Assemblies....Pages 177-196
Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique....Pages 197-231
Front Matter....Pages 233-233
Hierarchical Uncoupling-Coupling of Metastable Conformations....Pages 235-259
Automatic Identification of Metastable Conformations via Self-Organized Neural Networks....Pages 260-284
Front Matter....Pages 285-285
Equilibrium and Nonequilibrium Foundations of Free Energy Computational Methods....Pages 287-303
Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms....Pages 304-332
Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions....Pages 333-355
Front Matter....Pages 357-357
Treecode Algorithms for Computing Nonbonded Particle Interactions....Pages 359-380
A New Reciprocal Space Based Method for Treating Long Range Interactions in Ab Initio and Force-Field Based Calculations for Surfaces, Wires, and Clusters....Pages 381-410
Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking....Pages 411-441
Front Matter....Pages 443-443
Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model....Pages 445-476
Identification of Sequence-Specific Tertiary Packing Motifs in Protein Structures using Delaunay Tessellation....Pages 477-494
Back Matter....Pages 496-508

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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.
Content:
Front Matter....Pages I-IX
Front Matter....Pages 1-1
Methods for Macromolecular Modeling (M3): Assessment of Progress and Future Perspectives....Pages 3-27
Front Matter....Pages 29-29
Mathematics and Molecular Neurobiology....Pages 31-60
Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites....Pages 61-70
Front Matter....Pages 71-71
A Test Set for Molecular Dynamics Algorithms....Pages 73-103
Internal Coordinate Molecular Dynamics Based on the Spectroscopic B-Matrix....Pages 104-128
The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure....Pages 129-145
Overcoming Instabilities in Verlet-I/r-RESPA with the Mollified Impulse Method....Pages 146-174
Front Matter....Pages 175-175
On the Potential of Monte Carlo Methods for Simulating Macromolecular Assemblies....Pages 177-196
Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique....Pages 197-231
Front Matter....Pages 233-233
Hierarchical Uncoupling-Coupling of Metastable Conformations....Pages 235-259
Automatic Identification of Metastable Conformations via Self-Organized Neural Networks....Pages 260-284
Front Matter....Pages 285-285
Equilibrium and Nonequilibrium Foundations of Free Energy Computational Methods....Pages 287-303
Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms....Pages 304-332
Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions....Pages 333-355
Front Matter....Pages 357-357
Treecode Algorithms for Computing Nonbonded Particle Interactions....Pages 359-380
A New Reciprocal Space Based Method for Treating Long Range Interactions in Ab Initio and Force-Field Based Calculations for Surfaces, Wires, and Clusters....Pages 381-410
Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking....Pages 411-441
Front Matter....Pages 443-443
Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model....Pages 445-476
Identification of Sequence-Specific Tertiary Packing Motifs in Protein Structures using Delaunay Tessellation....Pages 477-494
Back Matter....Pages 496-508
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