Molecular dynamics simulations of large macromolecular complexes. (Q35768084)

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4 March 2020

review article

1 reference

title

Molecular dynamics simulations of large macromolecular complexes (English)

1 reference

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4 March 2020

1 reference

1

1 reference

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4 March 2020

Boon Chong Goh

2

1 reference

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4 March 2020

Hang Yu

7

1 reference

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4 March 2020

Zhe Wu

8

1 reference

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4 March 2020

author name string

C Keith Cassidy

3

1 reference

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4 March 2020

Bo Liu

4

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4 March 2020

Rafael C Bernardi

5

1 reference

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4 March 2020

Till Rudack

6

1 reference

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4 March 2020

Klaus Schulten

9

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4 March 2020

publication date

4 April 2015

1 reference

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Current Opinion in Structural Biology

4 March 2020

published in

1 reference

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4 March 2020

volume

31

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4 March 2020

page(s)

64-74

1 reference

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Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.

4 March 2020

cites work

1 reference

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Simulations show that virus assembly and budding are facilitated by membrane microdomains

12 July 2018

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Ultrastable cellulosome-adhesion complex tightens under load

12 July 2018

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Architecture and signal transduction mechanism of the bacterial chemosensory array: progress, controversies, and challenges

12 July 2018

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Molecular dynamics simulation: a tool for exploration and discovery using simple models

12 July 2018

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A tale of chromatin and transcription in 100 structures

12 July 2018

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Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution

12 July 2018

1 reference

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All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution.

12 July 2018

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The power of coarse graining in biomolecular simulations.

12 July 2018

1 reference

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Drug sensing by the ribosome induces translational arrest via active site perturbation

12 July 2018

1 reference

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Lipid cell biology. Polyunsaturated phospholipids facilitate membrane deformation and fission by endocytic proteins.

12 July 2018

1 reference

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Pathways for virus assembly around nucleic acids.

12 July 2018

1 reference

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Molecular dynamics study of enhanced Man5B enzymatic activity

12 July 2018

1 reference

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Macrolide antibiotics allosterically predispose the ribosome for translation arrest

12 July 2018

1 reference

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Light harvesting by lamellar chromatophores in Rhodospirillum photometricum

12 July 2018

1 reference

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High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis

12 July 2018

1 reference

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Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly

12 July 2018

1 reference

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Effect of microfibril twisting on theoretical powder diffraction patterns of cellulose Iβ

12 July 2018

1 reference

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Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating

12 July 2018

1 reference

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HIV-1 uncoating: connection to nuclear entry and regulation by host proteins

12 July 2018

1 reference

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Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides

12 July 2018

1 reference

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Cellular and molecular structure as a unifying framework for whole-cell modeling

12 July 2018

1 reference

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pH-induced stability switching of the bacteriophage HK97 maturation pathway

12 July 2018

1 reference

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Theoretical frameworks for multiscale modeling and simulation

12 July 2018

1 reference

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Integrated structural analysis of the human nuclear pore complex scaffold

12 July 2018

1 reference

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Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition

12 July 2018

1 reference

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Energy barriers and driving forces in tRNA translocation through the ribosome

12 July 2018

1 reference

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A two-pronged structural analysis of retroviral maturation indicates that core formation proceeds by a disassembly-reassembly pathway rather than a displacive transition.

12 July 2018

1 reference

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Protein-mediated transformation of lipid vesicles into tubular networks

12 July 2018

1 reference

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Viral genome structures are optimal for capsid assembly

12 July 2018

1 reference

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Impact of ribosomal modification on the binding of the antibiotic telithromycin using a combined grand canonical monte carlo/molecular dynamics simulation approach

12 July 2018

1 reference

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Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

12 July 2018

1 reference

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Perspective on the Martini model.

12 July 2018

1 reference

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Structures of the human and Drosophila 80S ribosome

12 July 2018

1 reference

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Connecting the kinetics and energy landscape of tRNA translocation on the ribosome

12 July 2018

1 reference

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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

12 July 2018

1 reference

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Membrane sculpting by F-BAR domains studied by molecular dynamics simulations

12 July 2018

1 reference

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Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography

12 July 2018

1 reference

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Early stages of the HIV-1 capsid protein lattice formation

12 July 2018

1 reference

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Surveying capsid assembly pathways through simulation-based data fitting

12 July 2018

1 reference

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Electrically induced conformational change of peptides on metallic nanosurfaces

12 July 2018

1 reference

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A whole-cell computational model predicts phenotype from genotype

12 July 2018

1 reference

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Virus capsid dissolution studied by microsecond molecular dynamics simulations

12 July 2018

1 reference

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Structural basis of membrane bending by the N-BAR protein endophilin

12 July 2018

1 reference

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fSUB: normal mode analysis with flexible substructures

12 July 2018

1 reference

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12 July 2018

1 reference

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Computational studies of molecular machines: the ribosome

12 July 2018

1 reference

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A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome

12 July 2018

1 reference

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Key structural features of the actin filament Arp2/3 complex branch junction revealed by molecular simulation

12 July 2018

1 reference

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Global landscape of HIV-human protein complexes

12 July 2018

1 reference

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Simulations of nuclear pore transport yield mechanistic insights and quantitative predictions

12 July 2018

1 reference

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Simulated self-assembly of the HIV-1 capsid: protein shape and native contacts are sufficient for two-dimensional lattice formation

12 July 2018

1 reference

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Biomass pretreatment: fundamentals toward application.

12 July 2018

1 reference

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Cryo-EM structure of the ribosome–SecYE complex in the membrane environment

12 July 2018

1 reference

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The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation

12 July 2018

1 reference

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Normal mode analysis and applications in biological physics

12 July 2018

1 reference

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Applications of computational science for understanding enzymatic deconstruction of cellulose

12 July 2018

1 reference

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Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale.

12 July 2018

1 reference

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All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling

12 July 2018

1 reference

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Control of actin filament treadmilling in cell motility

12 July 2018

1 reference

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The role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized mesoporous silica surfaces

12 July 2018

1 reference

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Discovery through the computational microscope

12 July 2018

1 reference

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Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography

12 July 2018

1 reference

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12 July 2018

1 reference

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Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Four-scale description of membrane sculpting by BAR domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Structural basis of membrane invagination by F-BAR domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

The structural basis of actin filament branching by the Arp2/3 complex

12 July 2018

1 reference

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Disassembly of nanodiscs with cholate

12 July 2018

1 reference

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Regulation of actin filament assembly by Arp2/3 complex and formins

12 July 2018

1 reference

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Biomass recalcitrance: engineering plants and enzymes for biofuels production

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

12 July 2018

1 reference

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The bacterial ribosome as a target for antibiotics

12 July 2018

1 reference

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Scalable molecular dynamics with NAMD

12 July 2018

1 reference

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Constant pH molecular dynamics with proton tautomerism

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Classification of orally administered drugs on the World Health Organization Model list of Essential Medicines according to the biopharmaceutics classification system

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Molecular biomimetics: nanotechnology through biology

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

25 years of the WHO essential medicines lists: progress and challenges

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

The structures of four macrolide antibiotics bound to the large ribosomal subunit

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

A ratchet-like inter-subunit reorganization of the ribosome during translocation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

All-atom molecular dynamics simulation of a photosystem i/detergent complex.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Lipid organization of the plasma membrane

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Influence of thiostrepton binding on the ribosomal GTPase associated region characterized by molecular dynamics simulation.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Stochastic gating and drug-ribosome interactions.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Investigation of a predicted N-terminal amphipathic α-helix using atomistic molecular dynamics simulation of a complete prototype poliovirus virion

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation

15 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4476923

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation

15 November 2018

1 reference

12 December 2020

Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic

1 reference

12 December 2020

Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles

1 reference

12 December 2020

Solvent-driven preferential association of lignin with regions of crystalline cellulose in molecular dynamics simulation

1 reference

12 December 2020

10.1016/J.SBI.2015.03.007

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25845770%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25845770%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

1 reference