A natural coarse graining for simulating large biomolecular motion
about
Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunitsMechanical and assembly units of viral capsids identified via quasi-rigid domain decompositionMethod for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration.Can morphing methods predict intermediate structures?Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.Iterative cluster-NMA: A tool for generating conformational transitions in proteins.Order parameters for macromolecules: application to multiscale simulation.Hierarchical Multiscale Modeling of Macromolecules and their AssembliesTracing conformational changes in proteins.Theoretical frameworks for multiscale modeling and simulationCoarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.Stability of graph communities across time scales.Studying functional dynamics in bio-molecules using accelerated molecular dynamics.Comparative study of various normal mode analysis techniques based on partial Hessians.Performance of protein disorder prediction programs on amino acid substitutions.Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order ParametersMicroseconds dynamics simulations of the outer-membrane protease TNormal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic modelsA Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces.A systematic methodology for defining coarse-grained sites in large biomoleculesMultiscale macromolecular simulation: role of evolving ensembles.Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures.Rigidity percolation and the spatial heterogeneity of soft modes in disordered materialsComputational methods for predicting sites of functionally important dynamics.Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining.Perspective: Coarse-grained models for biomolecular systems.Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer.Rigidity versus flexibility: the dilemma of understanding protein thermal stability.Global and local indices for characterizing biomolecular flexibility and rigidity.Predicting the open conformations of protein kinases using molecular dynamics simulations.Sophisticated modeling uncovers atomic DNA structure in bacteriophage φ29 cavity.Substrate-modulated thermal fluctuations affect long-range allosteric signaling in protein homodimers: exemplified in CAP.Analyzing the flexibility of RNA structures by constraint counting.Protein folding pathways and state transitions described by classical equations of motion of an elastic network model.Sequence composition and environment effects on residue fluctuations in protein structures.Protein rigidity and thermophilic adaptation.The multiscale coarse-graining method. VIII. Multiresolution hierarchical basis functions and basis function selection in the construction of coarse-grained force fields.The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems.
P2860
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P2860
A natural coarse graining for simulating large biomolecular motion
description
2006 nî lūn-bûn
@nan
2006 թուականի Յունիսին հրատարակուած գիտական յօդուած
@hyw
2006 թվականի հունիսին հրատարակված գիտական հոդված
@hy
2006年の論文
@ja
2006年論文
@yue
2006年論文
@zh-hant
2006年論文
@zh-hk
2006年論文
@zh-mo
2006年論文
@zh-tw
2006年论文
@wuu
name
A natural coarse graining for simulating large biomolecular motion
@ast
A natural coarse graining for simulating large biomolecular motion
@en
type
label
A natural coarse graining for simulating large biomolecular motion
@ast
A natural coarse graining for simulating large biomolecular motion
@en
prefLabel
A natural coarse graining for simulating large biomolecular motion
@ast
A natural coarse graining for simulating large biomolecular motion
@en
P2860
P1433
P1476
A natural coarse graining for simulating large biomolecular motion
@en
P2093
Holger Gohlke
M F Thorpe
P2860
P304
P356
10.1529/BIOPHYSJ.106.083568
P407
P577
2006-06-30T00:00:00Z