(Q37077825)

18 August 2017

Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies (English)

1 reference

18 August 2017

1 reference

Abhishek Singharoy

1

1 reference

18 August 2017

Harshad Joshi

series ordinal

2

1 reference

18 August 2017

Yinglong Miao

series ordinal

3

1 reference

18 August 2017

Peter J Ortoleva

series ordinal

4

1 reference

18 August 2017

language of work or name

English

0 references

publication date

9 March 2012

1 reference

Journal of Physical Chemistry B

18 August 2017

1 reference

18 August 2017

116

1 reference

18 August 2017

29

1 reference

18 August 2017

8423-8434

1 reference

The role of collective motion in examples of coarsening and self-assembly.

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Multiscale simulation of microbe structure and dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Relative stability of de novo four-helix bundle proteins: insights from coarse grained molecular simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Order parameters for macromolecules: application to multiscale simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Multiscale analytic continuation approach to nanosystem simulation: applications to virus electrostatics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Thermal nanostructure: an order parameter multiscale ensemble approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Long-timescale molecular dynamics simulations of protein structure and function.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Invariant polymorphism in virus capsid assembly

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Molecular dynamics/order parameter extrapolation for bionanosystem simulations.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Stochastic dynamics of bionanosystems: Multiscale analysis and specialized ensembles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Multiscale modeling of biomolecular systems: in serial and in parallel

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Core-controlled polymorphism in virus-like particles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Multiscale simulation of transmembrane proteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

A natural coarse graining for simulating large biomolecular motion

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

The structural and functional role of RNA in icosahedral virus assembly

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Simulating materials failure by using up to one billion atoms and the world's fastest computer: Brittle fracture

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Scalable molecular dynamics with NAMD

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Coarse-grained normal mode analysis in structural biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Biophysical studies on the RNA cores of satellite tobacco mosaic virus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Investigating protein dynamics in collective coordinate space

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Essential dynamics of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

A thermodynamic study of unusually stable RNA and DNA hairpins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Analysis of rapid, large-scale protein quaternary structural changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NomegaV) maturation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Quasi-harmonic method for studying very low frequency modes in proteins.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Liquid-crystal transitions: a first-principles multiscale approach.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Self-assembly of nanocomponents into composite structures: derivation and simulation of Langevin equations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Multiscale theory of collective and quasiparticle modes in quantum nanosystems.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Normal mode partitioning of Langevin dynamics for biomolecules

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Viral structural transitions: an all-atom multiscale theory.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

All-atom multiscaling and new ensembles for dynamical nanoparticles.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Collective Langevin dynamics of conformational motions in proteins.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Modeling large-scale dynamics of proteins.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4937887

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis

4 December 2018

1 reference

12 December 2020

New space warping method for the simulation of large-scale macromolecular conformational changes

1 reference

12 December 2020

Dynamical structure functions, collective modes, and energy gap in charged-particle bilayers

1 reference

12 December 2020

HiRE-RNA: a high resolution coarse-grained energy model for RNA

1 reference

12 December 2020

Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis

1 reference

12 December 2020

Software news and updates. Carma: a molecular dynamics analysis program

1 reference

12 December 2020

Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism

1 reference

12 December 2020

Excited-state lifetimes of far-infrared collective modes in proteins

1 reference

12 December 2020

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

1 reference

12 December 2020

Molecular Dynamics Simulation of the Structure, Dynamics, and Thermostability of the RNA Hairpins uCACGg and cUUCGg

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP2119247

1 reference

18 August 2017

1 reference

18 August 2017

PubMed publication ID

22356532

1 reference