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

Front Matter....Pages I-IX
Front Matter....Pages 1-1
Methods for Macromolecular Modeling (M 3 ): 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