(Q42380595)

28 October 2017

Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber (English)

1 reference

28 October 2017

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Alexey Onufriev

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

author name string

Saeed Izadi

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

publication date

17 October 2016

1 reference

Journal of Chemical Theory and Computation

28 October 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

volume

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

issue

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

page(s)

5946-5959

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

Accuracy limit of rigid 3-point water models

2 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Subnucleosomal structures and nucleosome asymmetry across a genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

The polymorphisms of the chromatin fiber.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Building Water Models: A Different Approach

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Point charges optimally placed to represent the multipole expansion of charge distributions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Modelling chromatin structure and dynamics: status and prospects

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Toward convergence of experimental studies and theoretical modeling of the chromatin fiber

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

How fast-folding proteins fold

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Generalized Born model with a simple, robust molecular volume correction

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Charge State of the Globular Histone Core Controls Stability of the Nucleosome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Characterization of the N-terminal tail domain of histone H3 in condensed nucleosome arrays by hydrogen exchange and NMR.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Nucleosome destabilization in the epigenetic regulation of gene expression

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Chromatin fiber structure: Where is the problem now?

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Computational sidechain placement and protein mutagenesis with implicit solvent models.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

A generalized born implicit-membrane representation compared to experimental insertion free energies.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

A residue-pairwise generalized born scheme suitable for protein design calculations.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Molecular dynamics: survey of methods for simulating the activity of proteins

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Histone H4-K16 acetylation controls chromatin structure and protein interactions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

The Amber biomolecular simulation programs

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Nucleotide-dependent bending flexibility of tubulin regulates microtubule assembly

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Molecular dynamics and protein function

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

The ENCODE (ENCyclopedia Of DNA Elements) Project

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Recent advances in the development and application of implicit solvent models in biomolecule simulations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Exploring protein native states and large-scale conformational changes with a modified generalized born model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

The structure of DNA in the nucleosome core

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Molecular dynamics simulations of biomolecules

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Electrostatics of nanosystems: application to microtubules and the ribosome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Generalized born models of macromolecular solvation effects

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Calculations of proton-binding thermodynamics in proteins

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Crystal structure of the nucleosome core particle at 2.8 A resolution

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

VMD: visual molecular dynamics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Classical electrostatics in biology and chemistry

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Theory of electrostatic interactions in macromolecules

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

The effects of truncating long-range forces on protein dynamics.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Radial density distribution of chromatin: evidence that chromatin fibers have solid centers

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

An n log n Generalized Born Approximation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

All-atom level direct folding simulation of a betabetaalpha miniprotein.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

FACTS: Fast analytical continuum treatment of solvation.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

The Gaussian Generalized Born model: application to small molecules.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Analytical electrostatics for biomolecules: beyond the generalized Born approximation

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Implicit solvation based on generalized Born theory in different dielectric environments

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Generalized born model with a simple smoothing function.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Protein molecular dynamics with the generalized born/ACE solvent model

16 August 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

3 November 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

1 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5649046

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

1 December 2018

1 reference

12 December 2020

The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays

1 reference

12 December 2020

Hybrid trypsinized nucleosomal arrays: identification of multiple functional roles of the H2A/H2B and H3/H4 N-termini in chromatin fiber compaction

1 reference

12 December 2020

Nucleosome structure and function

1 reference

12 December 2020

Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

12 December 2020

Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity

1 reference

12 December 2020

Identifiers

DOI

10.1021/ACS.JCTC.6B00712

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27748599%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

PubMed publication ID

27748599

1 reference