Multiscale methods for macromolecular simulations. (Q37250018)

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12 January 2020

review article

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title

Multiscale methods for macromolecular simulations (English)

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12 January 2020

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3

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12 January 2020

Paul Sherwood

series ordinal

1

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12 January 2020

author name string

Bernard R Brooks

series ordinal

2

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12 January 2020

publication date

17 September 2008

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Current Opinion in Structural Biology

12 January 2020

published in

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12 January 2020

volume

18

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12 January 2020

issue

5

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12 January 2020

page(s)

630-640

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A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.

12 January 2020

cites work

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12 December 2020

Understanding nature's design for a nanosyringe

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12 December 2020

"Learn on the fly": a hybrid classical and quantum-mechanical molecular dynamics simulation.

1 reference

12 December 2020

Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins

1 reference

12 December 2020

Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study

1 reference

12 December 2020

Coarse-grained models for proteins

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12 December 2020

Coarse-grained normal mode analysis in structural biology

1 reference

12 December 2020

Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy

1 reference

12 December 2020

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

1 reference

12 December 2020

Insertion and assembly of membrane proteins via simulation.

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12 December 2020

Coarse grained protein-lipid model with application to lipoprotein particles

1 reference

12 December 2020

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

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12 December 2020

A natural coarse graining for simulating large biomolecular motion

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12 December 2020

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

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12 December 2020

High-accuracy computation of reaction barriers in enzymes.

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12 December 2020

A voltage-sensor water pore

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12 December 2020

SGTx1, a Kv channel gating-modifier toxin, binds to the interfacial region of lipid bilayers

1 reference

12 December 2020

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

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12 December 2020

Mutagenesis and modeling of the peroxiredoxin (Prx) complex with the NMR structure of ATP-bound human sulfiredoxin implicate aspartate 187 of Prx I as the catalytic residue in ATP hydrolysis

1 reference

12 December 2020

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa.

1 reference

12 December 2020

Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations.

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12 December 2020

How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain.

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12 December 2020

Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.

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12 December 2020

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

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12 December 2020

Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model

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12 December 2020

Multiscale modeling of biomolecular systems: in serial and in parallel

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12 December 2020

Calculation of redox properties: understanding short- and long-range effects in rubredoxin

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12 December 2020

Coarse-grained peptide modeling using a systematic multiscale approach

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12 December 2020

How well can we understand large-scale protein motions using normal modes of elastic network models?

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12 December 2020

Aggregation and vesiculation of membrane proteins by curvature-mediated interactions

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12 December 2020

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

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12 December 2020

Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms

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12 December 2020

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

1 reference

12 December 2020

The MARTINI force field: coarse grained model for biomolecular simulations

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12 December 2020

Protein conformational transitions explored by mixed elastic network models.

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12 December 2020

G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers

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12 December 2020

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

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12 December 2020

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

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12 December 2020

Structural determinants of lateral gate opening in the protein translocon

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12 December 2020

Microseconds dynamics simulations of the outer-membrane protease T

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12 December 2020

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions.

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12 December 2020

Dynamics of the acetylcholinesterase tetramer

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12 December 2020

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

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12 December 2020

The implementation of a fast and accurate QM/MM potential method in Amber

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12 December 2020

Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution

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12 December 2020

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

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12 December 2020

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies.

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12 December 2020

Mechanosensitive membrane channels in action

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12 December 2020

Coarse-grained simulation: a high-throughput computational approach to membrane proteins

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12 December 2020

A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations

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12 December 2020

Coarse-grained force field for the nucleosome from self-consistent multiscaling

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12 December 2020

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes

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12 December 2020

Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations

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12 December 2020

Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles

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12 December 2020

Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach.

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12 December 2020

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods

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12 December 2020

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

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12 December 2020

The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.

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12 December 2020

Four-scale description of membrane sculpting by BAR domains

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12 December 2020

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

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12 December 2020

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

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12 December 2020

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

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12 December 2020

Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants

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12 December 2020

10.1016/J.SBI.2008.07.003

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18721882%20AND%20SRC:MED&resulttype=core&format=json

12 January 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18721882%20AND%20SRC:MED&resulttype=core&format=json

12 January 2020

PubMed publication ID

18721882

1 reference