Computational Methods for Macromolecules: Challenges and Applications: Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, October 12–14, 2000Tamar Schlick, Hin Hark Gan Springer Science & Business Media, 6 thg 8, 2002 - 504 trang 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. |
Nội dung
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 |
Ấn bản in khác - Xem tất cả
Computational Methods for Macromolecules: Challenges and Applications ... Tamar Schlick,Hin H. Gan Xem trước bị giới hạn - 2012 |
Computational Methods for Macromolecules: Challenges and Applications Tamar Schlick,Hin H Gan Không có bản xem trước - 2011 |
Thuật ngữ và cụm từ thông dụng
algorithm all-atom analysis approach approximation atoms average B-matrix Biol biomolecular C-terminus calculations charge Chem cluster Comp computational configuration convergence cutoff decoy defined density dielectric dihedral distribution efficient energy function ensemble enzyme equation error evaluation Ewald Ewald summation fast finite force field free energy grid Hartree hydrogen bond initio integration internal coordinates kcal/mol Lennard-Jones ligand linear macromolecular Markov chain matrix MD simulation metastable metastable sets method microstates molecular dynamics molecular dynamics simulations Monte Carlo Monte Carlo method motifs multicanonical native native-like obtained OPLS-AA/SGB optimization parameter particle peptide Phys potential energy problem protein folding protein structure QM/MM reaction receptor replica-exchange replicas residues RMSD Schlick scoring function screening function segment sequence Sigma Simulated Annealing solution solvation solvent space step summation surface Table techniques temperature tion torsion angles treecode UCMC umbrella sampling values vector Verlet-I/r-RESPA Voronoi tessellation water molecules