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Close encounters with DNAFrom residue coevolution to protein conformational ensembles and functional dynamics.A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inferenceNonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation DerivativesComparative Normal Mode Analysis of the Dynamics of DENV and ZIKV CapsidsApplications of computer-aided approaches in the development of hepatitis C antiviral agents.Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly.Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution.The ribosome's energy landscape: Recent insights from computationTheoretical frameworks for multiscale modeling and simulationStructure and conformational dynamics of scaffolded DNA origami nanoparticlesWeb-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems.COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino AcidsSimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins.Both piston-like and rotational motions are present in bacterial chemoreceptor signaling.Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systemsThe discrete multi-hybrid system for the simulation of solid-liquid flows.Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations.All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.Recent advances in transferable coarse-grained modeling of proteins.Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.Perspective: Coarse-grained models for biomolecular systems.Transferability of a coarse-grained atactic polystyrene model: the non-bonded potential effect.Data-driven coarse graining of large biomolecular structuresComputational studies of peptide-induced membrane pore formation.Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product developmentBayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps.Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides.The mystery of membrane organization: composition, regulation and roles of lipid rafts.Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents.
P2860
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P2860
description
article científic
@ca
article scientifique
@fr
articol științific
@ro
articolo scientifico
@it
artigo científico
@gl
artigo científico
@pt
artigo científico
@pt-br
artikel ilmiah
@id
artikull shkencor
@sq
artículo científico
@es
name
Coarse-graining methods for computational biology.
@en
type
label
Coarse-graining methods for computational biology.
@en
prefLabel
Coarse-graining methods for computational biology.
@en
P1476
Coarse-graining methods for computational biology.
@en
P2093
Marissa G Saunders
P356
10.1146/ANNUREV-BIOPHYS-083012-130348
P577
2013-02-28T00:00:00Z