Computational Methods for Macromolecules: Challenges and Applications

Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, October 12-14, 2000

520 Seiten, Taschenbuch

Kurzbeschreibung des Verlags

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.

• Reihe: Lecture Notes in Computational Science and Engineering
• Themen: Mathematik und Naturwissenschaften Mathematik Angewandte Mathematik Mathematische Modellierung
• ISBN: 9783540437567
• Sprache: Englisch
• Erscheinungsdatum: 06.08.2002
• Größe: 235 x 155 mm
• Verlag: Springer Vieweg
• Herausgegeben von: Hin H. Gan, Tamar Schlick