Perspective: Coarse-grained models for biomolecular systems (Q38136697)

29 August 2017

title

Perspective: Coarse-grained models for biomolecular systems (English)

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29 August 2017

W G Noid

1

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29 August 2017

language of work or name

English

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publication date

1 September 2013

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Journal of Chemical Physics

29 August 2017

published in

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29 August 2017

volume

139

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29 August 2017

issue

9

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29 August 2017

page(s)

090901

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29 August 2017

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Biomolecularmodeling and simulation: a field coming of age.

21 January 2018

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Coarse grain models and the computer simulation of soft materials

21 January 2018

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Multiscale modeling of biomolecular systems: in serial and in parallel

21 January 2018

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Coarse-grained models of protein folding: toy models or predictive tools?

21 January 2018

1 reference

Multiscale methods for macromolecular simulations.

21 January 2018

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Multiscale modeling of emergent materials: biological and soft matter

21 January 2018

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Multiscale simulation of soft matter systems

21 January 2018

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Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome

21 January 2018

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Capturing the essence of folding and functions of biomolecules using coarse-grained models

21 January 2018

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Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems

21 January 2018

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Coarse-grained molecular simulations of large biomolecules

21 January 2018

1 reference

On developing coarse-grained models for biomolecular simulation: a review

21 January 2018

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Coarse-graining methods for computational biology

21 January 2018

1 reference

Concurrent dual-resolution Monte Carlo simulation of liquid methane.

21 January 2018

1 reference

Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

21 January 2018

1 reference

Multiscale simulation of soft matter: from scale bridging to adaptive resolution

21 January 2018

1 reference

Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations.

21 January 2018

1 reference

Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics.

21 January 2018

1 reference

Recent progress in adaptive multiscale molecular dynamics simulations of soft matter.

21 January 2018

1 reference

Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer

21 January 2018

1 reference

Simulations of nucleation and elongation of amyloid fibrils

21 January 2018

1 reference

The Theory of Ultra-Coarse-Graining. 1. General Principles

21 January 2018

1 reference

The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems

21 January 2018

1 reference

A graph-theory algorithm for rapid protein side-chain prediction

21 January 2018

1 reference

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace.

21 January 2018

1 reference

Fast procedure for reconstruction of full-atom protein models from reduced representations.

21 January 2018

1 reference

PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

21 January 2018

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Coarse-grained model of nucleic acid bases.

21 January 2018

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Systematic multiscale simulation of membrane protein systems

21 January 2018

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Coarse-graining of multiprotein assemblies

21 January 2018

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A natural coarse graining for simulating large biomolecular motion

21 January 2018

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A systematic methodology for defining coarse-grained sites in large biomolecules

21 January 2018

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Optimal number of coarse-grained sites in different components of large biomolecular complexes.

21 January 2018

1 reference

Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits

21 January 2018

1 reference

Dynamics of essential collective motions in proteins: theory

21 January 2018

1 reference

Automatic domain decomposition of proteins by a Gaussian Network Model.

21 January 2018

1 reference

Stability and dynamics of virus capsids described by coarse-grained modeling

21 January 2018

1 reference

Four-scale description of membrane sculpting by BAR domains

21 January 2018

1 reference

Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data

21 January 2018

1 reference

Implicit solvent simulation models for biomembranes

21 January 2018

1 reference

Lipids on the move: simulations of membrane pores, domains, stalks and curves

21 January 2018

1 reference

Multiscale coarse-graining of monosaccharides.

21 January 2018

1 reference

Martini Coarse-Grained Force Field: Extension to Carbohydrates.

21 January 2018

1 reference

Dissecting force interactions in cellulose deconstruction reveals the required solvent versatility for overcoming biomass recalcitrance

21 January 2018

1 reference

Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water

21 January 2018

1 reference

Computer simulation of protein folding

21 January 2018

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A simplified representation of protein conformations for rapid simulation of protein folding

21 January 2018

1 reference

Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model

21 January 2018

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Metastability of the folded states of globular proteins

21 January 2018

1 reference

Coarse-grained sequences for protein folding and design

21 January 2018

1 reference

Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models

21 January 2018

1 reference

Global dynamics of proteins: bridging between structure and function

21 January 2018

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Biomolecular dynamics: order-disorder transitions and energy landscapes

21 January 2018

1 reference

Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

21 January 2018

1 reference

Coarse-grained force field: general folding theory

21 January 2018

1 reference

Protein-protein docking with a reduced protein model accounting for side-chain flexibility

21 January 2018

1 reference

Three-helix-bundle protein in a Ramachandran model

21 January 2018

1 reference

Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides

21 January 2018

1 reference

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

21 January 2018

1 reference

Effective potentials for folding proteins.

21 January 2018

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Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide.

21 January 2018

1 reference

Generic coarse-grained model for protein folding and aggregation.

21 January 2018

1 reference

Extending the PRIME model for protein aggregation to all 20 amino acids

21 January 2018

1 reference

The coarse-grained OPEP force field for non-amyloid and amyloid proteins.

21 January 2018

1 reference

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

21 January 2018

1 reference

Coarse-grained modeling of the actin filament derived from atomistic-scale simulations

21 January 2018

1 reference

Dynamic pathways for viral capsid assembly

21 January 2018

1 reference

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids

21 January 2018

1 reference

A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO).

21 January 2018

1 reference

Microtubule elasticity: connecting all-atom simulations with continuum mechanics

21 January 2018

1 reference

Minimalist models for protein folding and design

21 January 2018

1 reference

Coarse-grained models for proteins

21 January 2018

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Minimalist models for proteins: a comparative analysis

21 January 2018

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Coarse-grained models for protein aggregation.

21 January 2018

1 reference

Modeling superhelical DNA: recent analytical and dynamic approaches.

21 January 2018

1 reference

Simulating DNA at low resolution

21 January 2018

1 reference

Development of coarse-graining DNA models for single-nucleotide resolution analysis

21 January 2018

1 reference

Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

21 January 2018

1 reference

Chemically accurate coarse graining of double-stranded DNA.

21 January 2018

1 reference

Mesoscopic modeling for nucleic acid chain dynamics.

21 January 2018

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A mesoscale model of DNA and its renaturation

21 January 2018

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DNA nanotweezers studied with a coarse-grained model of DNA.

21 January 2018

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A coarse grain model for DNA.

21 January 2018

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Moving beyond Watson-Crick models of coarse grained DNA dynamics.

21 January 2018

1 reference

Sequence-dependent thermodynamics of a coarse-grained DNA model.

21 January 2018

1 reference

DNA and lipid bilayers: self-assembly and insertion

21 January 2018

1 reference

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

21 January 2018

1 reference

Insights on protein-DNA recognition by coarse grain modelling

21 January 2018

1 reference

Protein-DNA docking with a coarse-grained force field

21 January 2018

1 reference

Mechanical unfolding of RNA hairpins

21 January 2018

1 reference

Coarse-graining RNA nanostructures for molecular dynamics simulations.

21 January 2018

1 reference

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

21 January 2018

1 reference

Coarse-grained model for simulation of RNA three-dimensional structures.

21 January 2018

1 reference

A coarse-grained force field for Protein-RNA docking

21 January 2018

1 reference

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

21 January 2018

1 reference

Mechanical unfolding of RNA: from hairpins to structures with internal multiloops

21 January 2018

1 reference

Computational approaches to modeling viral structure and assembly

21 January 2018

1 reference

Coarse-grained simulations of macromolecules: from DNA to nanocomposites

21 January 2018

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Dominant forces in protein folding

21 January 2018

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Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA.

21 January 2018

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Representability problems for coarse-grained water potentials.

21 January 2018

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Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy

21 January 2018

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Water modeled as an intermediate element between carbon and silicon

21 January 2018

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Structural transformation in supercooled water controls the crystallization rate of ice.

21 January 2018

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Computer simulation of local order in condensed phases of silicon

21 January 2018

1 reference

Coarse-grain modelling of DMPC and DOPC lipid bilayers

21 January 2018

1 reference

A coarse-grained model of DNA with explicit solvation by water and ions

21 January 2018

1 reference

On the investigation of coarse-grained models for water: balancing computational efficiency and the retention of structural properties

21 January 2018

1 reference

From Molecular Dynamics to Dissipative Particle Dynamics

21 January 2018

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Coarse graining of nonbonded degrees of freedom.

21 January 2018

1 reference

On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models.

21 January 2018

1 reference

Polarizable water model for the coarse-grained MARTINI force field

21 January 2018

1 reference

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations

21 January 2018

1 reference

Combining a polarizable force-field and a coarse-grained polarizable solvent model: application to long dynamics simulations of bovine pancreatic trypsin inhibitor.

21 January 2018

1 reference

A new coarse-grained model for water: the importance of electrostatic interactions.

21 January 2018

1 reference

Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations

21 January 2018

1 reference

Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B.

21 January 2018

1 reference

Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition

21 January 2018

1 reference

Solvent-free lipid bilayer model using multiscale coarse-graining

21 January 2018

1 reference

A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations

21 January 2018

1 reference

Recent advances in implicit solvent-based methods for biomolecular simulations

21 January 2018

1 reference

Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications

21 January 2018

1 reference

Coarse-Grained Molecular Models of Water: A Review

21 January 2018

1 reference

Modeling water, the hydrophobic effect, and ion solvation

21 January 2018

1 reference

Interfaces and the driving force of hydrophobic assembly

21 January 2018

1 reference

Toy amphiphiles on the computer: What can we learn from generic models?

21 January 2018

1 reference

Computer simulations of self-assembled membranes

21 January 2018

1 reference

Main phase transition in lipid bilayers: Phase coexistence and line tension in a soft, solvent-free, coarse-grained model.

21 January 2018

1 reference

Effect of beta-sheet propensity on peptide aggregation

21 January 2018

1 reference

Origins of structure in globular proteins

21 January 2018

1 reference

Simple simulations of DNA condensation

21 January 2018

1 reference

The MARTINI force field: coarse grained model for biomolecular simulations

21 January 2018

1 reference

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

21 January 2018

1 reference

Perspective on the Martini model.

21 January 2018

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The MARTINI Coarse-Grained Force Field: Extension to Proteins.

21 January 2018

1 reference

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

21 January 2018

1 reference

A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.

21 January 2018

1 reference

Memory Effects in Irreversible Thermodynamics

21 January 2018

1 reference

Mori-Zwanzig formalism as a practical computational tool.

21 January 2018

1 reference

Effective interactions in soft condensed matter physics

21 January 2018

1 reference

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

21 January 2018

1 reference

Polymer principles in protein structure and stability.

21 January 2018

1 reference

Basic ingredients of free energy calculations: a review

21 January 2018

1 reference

Announcing the worldwide Protein Data Bank

21 January 2018

1 reference

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

21 January 2018

1 reference

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

Analysis of domain motions by approximate normal mode calculations

21 January 2018

1 reference

Anisotropy of fluctuation dynamics of proteins with an elastic network model

21 January 2018

1 reference

Statistical Thermodynamics of Random Networks [and Discussion]

21 January 2018

1 reference

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

21 January 2018

1 reference

Dynamics of proteins in crystals: comparison of experiment with simple models

21 January 2018

1 reference

Application of elastic network models to proteins in the crystalline state

21 January 2018

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Essential dynamics of proteins

21 January 2018

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Flexibility and packing in proteins

21 January 2018

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The role of shape in determining molecular motions

21 January 2018

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Predictions of protein flexibility: first-order measures

21 January 2018

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Physical arguments for distance-weighted interactions in elastic network models for proteins

21 January 2018

1 reference

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis

21 January 2018

1 reference

Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.

21 January 2018

1 reference

Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology

21 January 2018

1 reference

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

21 January 2018

1 reference

Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model

21 January 2018

1 reference

Systematic multiscale parameterization of heterogeneous elastic network models of proteins

21 January 2018

1 reference

Markov methods for hierarchical coarse-graining of large protein dynamics.

21 January 2018

1 reference

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

21 January 2018

1 reference

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

21 January 2018

1 reference

Coarse-grained free energy functions for studying protein conformational changes: a double-well network model

21 January 2018

1 reference

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

21 January 2018

1 reference

Protein conformational transitions explored by mixed elastic network models.

21 January 2018

1 reference

Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors.

21 January 2018

1 reference

A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

21 January 2018

1 reference

vGNM: a better model for understanding the dynamics of proteins in crystals

21 January 2018

1 reference

Structural flexibility in proteins: impact of the crystal environment

21 January 2018

1 reference

Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions.

21 January 2018

1 reference

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

21 January 2018

1 reference

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

21 January 2018

1 reference

Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data

21 January 2018

1 reference

Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution

21 January 2018

1 reference

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

21 January 2018

1 reference

Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle

21 January 2018

1 reference

Global ribosome motions revealed with elastic network model

21 January 2018

1 reference

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

21 January 2018

1 reference

Conformational change of proteins arising from normal mode calculations

21 January 2018

1 reference

A comparative study of motor-protein motions by using a simple elastic-network model

21 January 2018

1 reference

Representing receptor flexibility in ligand docking through relevant normal modes.

21 January 2018

1 reference

Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.

21 January 2018

1 reference

Automatic prediction of protein interactions with large scale motion

21 January 2018

1 reference

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

21 January 2018

1 reference

Anisotropic network model: systematic evaluation and a new web interface.

21 January 2018

1 reference

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

21 January 2018

1 reference

MAVENs: motion analysis and visualization of elastic networks and structural ensembles

21 January 2018

1 reference

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

21 January 2018

1 reference

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

21 January 2018

1 reference

Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling?

21 January 2018

1 reference

Folding funnels and frustration in off-lattice minimalist protein landscapes

21 January 2018

1 reference

Theoretical Studies of Protein Folding

21 January 2018

1 reference

Spin glasses and the statistical mechanics of protein folding

21 January 2018

1 reference

Funnels, pathways, and the energy landscape of protein folding: a synthesis

21 January 2018

1 reference

The limited role of nonnative contacts in the folding pathways of a lattice protein.

21 January 2018

1 reference

Protein folding funnels: a kinetic approach to the sequence-structure relationship

21 January 2018

1 reference

From Levinthal to pathways to funnels

21 January 2018

1 reference

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

21 January 2018

1 reference

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

21 January 2018

1 reference

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

21 January 2018

1 reference

Probing the folding free energy landscape of the Src-SH3 protein domain

21 January 2018

1 reference

Go-ing for the prediction of protein folding mechanisms

21 January 2018

1 reference

Development of a physics-based force field for the scoring and refinement of protein models

21 January 2018

1 reference

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

21 January 2018

1 reference

Contact order, transition state placement and the refolding rates of single domain proteins.

21 January 2018

1 reference

Keeping it in the family: folding studies of related proteins

21 January 2018

1 reference

Experimental evaluation of topological parameters determining protein-folding rates

21 January 2018

1 reference

Protein folding theory: from lattice to all-atom models

21 January 2018

1 reference

The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation

21 January 2018

1 reference

The origins of asymmetry in the folding transition states of protein L and protein G.

21 January 2018

1 reference

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

21 January 2018

1 reference

The effects of nonnative interactions on protein folding rates: theory and simulation

21 January 2018

1 reference

Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes

21 January 2018

1 reference

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins.

21 January 2018

1 reference

Three-body interactions improve the prediction of rate and mechanism in protein folding models

21 January 2018

1 reference

Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues

21 January 2018

1 reference

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

21 January 2018

1 reference

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

21 January 2018

1 reference

An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability

21 January 2018

1 reference

Theory of the molecular transfer model for proteins with applications to the folding of the src-SH3 domain

21 January 2018

1 reference

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

21 January 2018

1 reference

Dynamics of allosteric transitions in GroEL.

21 January 2018

1 reference

Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

21 January 2018

1 reference

How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations

21 January 2018

1 reference

Simulations of beta-hairpin folding confined to spherical pores using distributed computing

21 January 2018

1 reference

Molecular crowding enhances native state stability and refolding rates of globular proteins

21 January 2018

1 reference

Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins.

21 January 2018

1 reference

Selection of optimal variants of Gō-like models of proteins through studies of stretching

21 January 2018

1 reference

Protein topology determines binding mechanism

21 January 2018

1 reference

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

21 January 2018

1 reference

Binding-induced folding of a natively unstructured transcription factor.

21 January 2018

1 reference

Robustness of atomistic Gō models in predicting native-like folding intermediates

21 January 2018

1 reference

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

21 January 2018

1 reference

Insights from coarse-grained Gō models for protein folding and dynamics

21 January 2018

1 reference

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation

21 January 2018

1 reference

Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding

21 January 2018

1 reference

Multiscale investigation of chemical interference in proteins

21 January 2018

1 reference

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

21 January 2018

1 reference

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures

21 January 2018

1 reference

Structure-derived potentials and protein simulations

21 January 2018

1 reference

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

21 January 2018

1 reference

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

21 January 2018

1 reference

Knowledge-based scoring function to predict protein-ligand interactions.

21 January 2018

1 reference

Statistical potential for assessment and prediction of protein structures

21 January 2018

1 reference

A new generation of statistical potentials for proteins.

21 January 2018

1 reference

Trends in template/fragment-free protein structure prediction

21 January 2018

1 reference

Knowledge-based potential for the polypeptide backbone

21 January 2018

1 reference

Development of novel statistical potentials for protein fold recognition

21 January 2018

1 reference

OPUS-Rota: a fast and accurate method for side-chain modeling

21 January 2018

1 reference

GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction

21 January 2018

1 reference

Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment

21 January 2018

1 reference

Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations

21 January 2018

1 reference

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys.

21 January 2018

1 reference

An iterative method for extracting energy-like quantities from protein structures.

21 January 2018

1 reference

An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials.

21 January 2018

1 reference

Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back

21 January 2018

1 reference

A structure-based method for derivation of all-atom potentials for protein folding

21 January 2018

1 reference

High-resolution protein folding with a transferable potential

21 January 2018

1 reference

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

21 January 2018

1 reference

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

21 January 2018

1 reference

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

21 January 2018

1 reference

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

21 January 2018

1 reference

An empirical energy function for threading protein sequence through the folding motif

21 January 2018

1 reference

Comparison of database potentials and molecular mechanics force fields

21 January 2018

1 reference

Effective energy functions for protein structure prediction.

21 January 2018

1 reference

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

21 January 2018

1 reference

The limit of accuracy of protein modeling: influence of crystal packing on protein structure.

21 January 2018

1 reference

Protein function in the crystal

21 January 2018

1 reference

Statistical potentials extracted from protein structures: how accurate are they?

21 January 2018

1 reference

Variability of conformations at crystal contacts in BPTI represent true low-energy structures: correspondence among lattice packing and molecular dynamics structures

21 January 2018

1 reference

Boltzmann-type distribution of side-chain conformation in proteins

21 January 2018

1 reference

Relation between native ensembles and experimental structures of proteins

21 January 2018

1 reference

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

21 January 2018

1 reference

Recovering physical potentials from a model protein databank

21 January 2018

1 reference

Energy functions in de novo protein design: current challenges and future prospects

21 January 2018

1 reference

Contact potential that recognizes the correct folding of globular proteins

21 January 2018

1 reference

Optimal protein-folding codes from spin-glass theory

21 January 2018

1 reference

How to derive a protein folding potential? A new approach to an old problem

21 January 2018

1 reference

How optimization of potential functions affects protein folding

21 January 2018

1 reference

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

21 January 2018

1 reference

TOUCHSTONE II: a new approach to ab initio protein structure prediction

21 January 2018

1 reference

In quest of an empirical potential for protein structure prediction.

21 January 2018

1 reference

Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction

21 January 2018

1 reference

An improved protein decoy set for testing energy functions for protein structure prediction.

21 January 2018

1 reference

A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics

21 January 2018

1 reference

A coarse-grained protein force field for folding and structure prediction.

21 January 2018

1 reference

On the design and analysis of protein folding potentials.

21 January 2018

1 reference

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

1 reference

OPUS-Ca: a knowledge-based potential function requiring only Calpha positions

21 January 2018

1 reference

Genomics-aided structure prediction

21 January 2018

1 reference

Identification of direct residue contacts in protein-protein interaction by message passing

21 January 2018

1 reference

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

21 January 2018

1 reference

Protein 3D structure computed from evolutionary sequence variation

21 January 2018

1 reference

Toward high-resolution de novo structure prediction for small proteins.

21 January 2018

1 reference

CASP9 assessment of free modeling target predictions

21 January 2018

1 reference

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

21 January 2018

1 reference

Predicting novel protein folds by using FRAGFOLD.

21 January 2018

1 reference

Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints

21 January 2018

1 reference

I-TASSER: a unified platform for automated protein structure and function prediction

21 January 2018

1 reference

Toward protein tertiary structure recognition by means of associative memory hamiltonians

21 January 2018

1 reference

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing

21 January 2018

1 reference

Restriction versus guidance in protein structure prediction.

21 January 2018

1 reference

Multiscale characterization of protein conformational ensembles

21 January 2018

1 reference

Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials

21 January 2018

1 reference

Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin

21 January 2018

1 reference

Thermodynamic consistency in variable-level coarse graining of polymeric liquids.

21 January 2018

1 reference

Systematic methods for structurally consistent coarse-grained models

21 January 2018

1 reference

MagiC: Software Package for Multiscale Modeling.

21 January 2018

1 reference

Coarse-graining entropy, forces, and structures.

21 January 2018

1 reference

The inverse problem in classical statistical mechanics

21 January 2018

1 reference

Iterative predictor-corrector method for extraction of the pair interaction from structural data for dense classical liquids

21 January 2018

1 reference

Reverse Monte Carlo Simulation: A New Technique for the Determination of Disordered Structures

21 January 2018

1 reference

Optimized interactions for targeted self-assembly: application to a honeycomb lattice.

21 January 2018

1 reference

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation.

21 January 2018

1 reference

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields.

21 January 2018

1 reference

Generalized Yvon-Born-Green theory for molecular systems.

21 January 2018

1 reference

The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure.

21 January 2018

1 reference

Reference state for the generalized Yvon–Born–Green theory: Application for coarse-grained model of hydrophobic hydration

21 January 2018

1 reference

Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model

21 January 2018

1 reference

Deriving effective mesoscale potentials from atomistic simulations.

21 January 2018

1 reference

Coarse-grained modeling for macromolecular chemistry

21 January 2018

1 reference

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

21 January 2018

1 reference

A structurally relevant coarse-grained model for cholesterol

21 January 2018

1 reference

A coarse-grained model for amorphous and crystalline fatty acids

21 January 2018

1 reference

Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain

21 January 2018

1 reference

Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.

21 January 2018

1 reference

A test of systematic coarse-graining of molecular dynamics simulations: thermodynamic properties

21 January 2018

1 reference

Systematic coarse-graining of molecular models by the Newton inversion method

21 January 2018

1 reference

Coarse-grained model for phospholipid/cholesterol bilayer

21 January 2018

1 reference

Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.

21 January 2018

1 reference

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

21 January 2018

1 reference

Coarse-graining errors and numerical optimization using a relative entropy framework

21 January 2018

1 reference

On Information and Sufficiency

21 January 2018

1 reference

A stochastic optimization approach to coarse-graining using a relative-entropy framework

21 January 2018

1 reference

A new multiscale algorithm and its application to coarse-grained peptide models for self-assembly

21 January 2018

1 reference

Relative entropy as a universal metric for multiscale errors

21 January 2018

1 reference

Obtaining fully dynamic coarse-grained models from MD.

21 January 2018

1 reference

Multiscale coarse graining of liquid-state systems

21 January 2018

1 reference

Optimal prediction and the Mori-Zwanzig representation of irreversible processes

21 January 2018

1 reference

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

21 January 2018

1 reference

Multiscale coarse-graining and structural correlations: connections to liquid-state theory

21 January 2018

1 reference

Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively

21 January 2018

1 reference

Fitting coarse-grained distribution functions through an iterative force-matching method.

21 January 2018

1 reference

Systematic coarse-graining of a multicomponent lipid bilayer

21 January 2018

1 reference

Coarse-grained peptide modeling using a systematic multiscale approach

21 January 2018

1 reference

Multiscale coarse-graining of the protein energy landscape

21 January 2018

1 reference

Modeling real dynamics in the coarse-grained representation of condensed phase systems.

21 January 2018

1 reference

Numerical coarse-graining of fluid field theories

21 January 2018

1 reference

Studies in Molecular Dynamics. I. General Method

21 January 2018

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

1 reference

Development and testing of a general amber force field

21 January 2018

1 reference

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

21 January 2018

1 reference

Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 January 2018

1 reference

Improved side-chain torsion potentials for the Amber ff99SB protein force field

21 January 2018

1 reference

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

21 January 2018

1 reference

Computational techniques for efficient conformational sampling of proteins

21 January 2018

1 reference

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

21 January 2018

1 reference

Equilibrium sampling in biomolecular simulations

21 January 2018

1 reference

Atomic-Level Characterization of the Structural Dynamics of Proteins

21 January 2018

1 reference

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

21 January 2018

1 reference

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

21 January 2018

1 reference

CHARMM: the biomolecular simulation program

21 January 2018

1 reference

Scalable molecular dynamics with NAMD

21 January 2018

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

21 January 2018

1 reference

Force field bias in protein folding simulations

21 January 2018

1 reference

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

21 January 2018

1 reference

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

21 January 2018

1 reference

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

21 January 2018

1 reference

Systematic validation of protein force fields against experimental data

21 January 2018

1 reference

Polarization effects in molecular mechanical force fields

21 January 2018

1 reference

Simulating water with rigid non-polarizable models: a general perspective

21 January 2018

1 reference

21 January 2018

Polarizable force fields

1 reference

Polarizable Force Fields: History, Test Cases, and Prospects

21 January 2018

1 reference

Current status of the AMOEBA polarizable force field

21 January 2018

1 reference

Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects

21 January 2018

1 reference

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

21 January 2018

1 reference

Let's get honest about sampling.

21 January 2018

1 reference

Speed up of dynamic observables in coarse-grained molecular-dynamics simulations of unentangled polymers.

21 January 2018

1 reference

Dynamic evolution in coarse-grained molecular dynamics simulations of polyethylene melts.

21 January 2018

1 reference

Large-scale molecular dynamics simulations of self-assembling systems.

21 January 2018

1 reference

Modeling the lipid component of membranes

21 January 2018

1 reference

On the formation of protein tertiary structure on a computer

21 January 2018

1 reference

A computer model to dynamically simulate protein folding: studies with crambin.

21 January 2018

1 reference

Potential energy functions for protein design.

21 January 2018

1 reference

Coarse-grained modeling of simple molecules at different resolutions in the absence of good sampling.

21 January 2018

1 reference

Hamiltonian adaptive resolution simulation for molecular liquids.

21 January 2018

1 reference

A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements.

21 January 2018

1 reference

A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

21 January 2018

1 reference

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains

21 January 2018

1 reference

Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis

21 January 2018

1 reference

Statistical mechanics of coarse graining: estimating dynamical speedups from excess entropies.

21 January 2018

1 reference

Minimizing memory as an objective for coarse-graining

21 January 2018

1 reference

Predicting the thermodynamics by using state-dependent interactions

21 January 2018

1 reference

Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints

21 January 2018

1 reference

The multiscale coarse-graining method. V. Isothermal-isobaric ensemble

21 January 2018

1 reference

Derivation of coarse grained models for multiscale simulation of liquid crystalline phase transitions

21 January 2018

1 reference

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

21 January 2018

1 reference

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

21 January 2018

1 reference

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.

21 January 2018

1 reference

The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials.

21 January 2018

1 reference

Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane.

21 January 2018

1 reference

A novel algorithm for creating coarse-grained, density dependent implicit solvent models

21 January 2018

1 reference

The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials

21 January 2018

1 reference

Supercoiling and Local Denaturation of Plasmids with a Minimalist DNA Model

21 January 2018

1 reference

Transferable Potentials for Phase Equilibria−Coarse-Grain Description for Linear Alkanes

21 January 2018

1 reference

Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics

21 January 2018

1 reference

Harmonicity in slow protein dynamics

21 January 2018

1 reference

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

21 January 2018

1 reference

Novel knowledge-based mean force potential at atomic level

21 January 2018

1 reference

Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures

21 January 2018

1 reference

Maximum Entropy Approach for Deducing Amino Acid Interactions in Proteins

21 January 2018

1 reference

Simple models for complex nonequilibrium fluids

21 January 2018

1 reference

Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins

21 January 2018

1 reference

A refined hydrogen bond potential for flexible protein models

21 January 2018

1 reference

On the microscopic foundation of dissipative particle dynamics

21 January 2018

1 reference

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

21 January 2018

1 reference

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?

21 January 2018

1 reference

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization

21 January 2018

1 reference

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.4818908

1 reference

29 August 2017

1 reference