Computational Methods for Macromolecules: Challenges and Applications: Challenges and Applications ; Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, October 12 - 14, 2000 ; with 55 Tables

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Tamar Schlick, Hin Hark Gan
Springer Science & Business Media, Aug 6, 2002 - Mathematics - 504 pages
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3 The workshop on Methods for Macromolecular Modeling (M ) , held at New York University on 12- 14 October 2000, attracted 187 participants from Eu rope, Asia, the Americas, and the Middle East. (see monod.biomath .nyu.eduj rvhganjconfOO.html for more information). The exciting program was made possible by the dedicated work of the international advisory committee whose members were P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, T. Schlick, and R. Skeel. We are indebted to the following agen cies and institutions for their generous support: the Burroughs Wellcome Fund, Department of Energy, National Science Foundation, National Insti tutes of Health, Computational Biomedicine Initiative at Mount Sinai School of Medicine, and NYU's Courant Institute of Mathematical Sciences, Depart ment of Chemistry, and Science Council. This volume is a collection of 19 review and original articles by the speak 3 ers and participants of the M workshop. The topics covered include molecu lar dynamics methods, Monte Carlo methods, other conformational sampling methods, free energy methods, long range interactions and fast electrostatics, and statistical approaches to protein structures. A perspective article intro duces the contributions in this volume and reflects on future prospects in macromolecular modeling.
  

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Contents

Mathematics and Molecular Neurobiology
31
Structural and Dynamical Characterization of Nuclei Acid Water and Ion Binding Sites
61
MOLECULAR DYNAMICS METHODS
71
A Test Set for Molecular Dynamics Algorithms
73
Internal Coordinate Molecular Dynamics Based on the Spectroscopic BMatrix
104
The Sigma MD Program and a Generic Interface Applicable to MultiFunctional Programs with Complex Hierarchical Command Structure
129
Overcoming Instabilities in VerletIrRESPA with the Mollified Impulse Method
146
MONTE CARLO METHODS
175
FREE ENERGY METHODS
285
Equilibrium and Nonequilibrium Foundations of Free Energy Computational Methods
287
FreeEnergy Calculations in Protein Folding by GeneralizedEnsemble Algorithms
304
Ab Initio QMMM and Free Energy Calculations of Enzyme Reactions
333
LONG RANGE INTERACTIONS AND FAST ELECTROSTATICS METHODS
357
Treecode Algorithms for Computing Nonbonded Particle Interactions
359
A New Reciprocal Space Based Method for Treating Long Range Interactions in Ab Initio and ForceField Based Calculations for Surfaces Wires and ...
381
Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking
411

On the Potential of Monte Carlo Methods for Simulating Macromolecular Assemblies
177
A Simulated Annealing Monte Carlo combined with Biased Scaled Collective Variables Technique
197
OTHER CONFORMATIONAL SAMPLING METHODS
233
Hierarchical UncouplingCoupling of Metastable Conformations
235
Automatic Identification of Metastable Conformations via SelfOrganized Neural Networks
260
STATISTICAL APPROACHES TO PROTEIN STRUCTURES
443
Fold Recognition using the OPLS AllAtom Potential and the Surface Generalized Born Solvent Model
445
Identification of SequenceSpecific Tertiary Packing Motifs in Protein Structures using Delaunay Tessellation
477
Color Plates
495
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