(Q34562935)

3 August 2017

Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping (English)

1 reference

3 August 2017

1 reference

1 reference

Stephen D Levene

4

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author name string

Stefan M Giovan

series ordinal

1

1 reference

3 August 2017

Robert G Scharein

series ordinal

2

1 reference

3 August 2017

Andreas Hanke

series ordinal

3

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3 August 2017

language of work or name

English

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publication date

1 November 2014

1 reference

Journal of Chemical Physics

3 August 2017

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3 August 2017

141

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3 August 2017

174902

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3 August 2017

17

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Creative Commons Attribution 3.0 Unported

3 August 2017

start time

5 November 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

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FtsK-dependent XerCD-dif recombination unlinks replication catenanes in a stepwise manner

7 July 2018

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7 July 2018

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7 July 2018

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Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells

7 July 2018

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Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

7 July 2018

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Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

7 July 2018

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Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers

7 July 2018

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A generalized G-SFED continuum solvation free energy calculation model

7 July 2018

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CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice

7 July 2018

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Distant activation of transcription: mechanisms of enhancer action

7 July 2018

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The long-range interaction landscape of gene promoters

7 July 2018

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XPG and XPF endonucleases trigger chromatin looping and DNA demethylation for accurate expression of activated genes

7 July 2018

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Measurements of DNA-loop formation via Cre-mediated recombination.

7 July 2018

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Biomolecular simulation: a computational microscope for molecular biology

7 July 2018

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DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage

7 July 2018

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Atomic force microscopy captures MutS tetramers initiating DNA mismatch repair.

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Equilibrium sampling in biomolecular simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

The nuts and bolts of ring-translocase structure and mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Roles of DNA looping in enhancer-blocking activity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Rapid sampling of all-atom peptides using a library-based polymer-growth approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Entropy as the driver of chromosome segregation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Cell type specificity of chromatin organization mediated by CTCF and cohesin.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Basic ingredients of free energy calculations: a review

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Alchemical free energy simulations for biological complexes: powerful but temperamental....

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding

7 July 2018

1 reference

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Absolute free energies estimated by combining precalculated molecular fragment libraries

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Collapse transition in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

DNA supercoiling inhibits DNA knotting

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Entropy and free energy of a mobile protein loop in explicit water

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

RNA folding: conformational statistics, folding kinetics, and ion electrostatics.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Discrete state model and accurate estimation of loop entropy of RNA secondary structures.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Extraction of configurational entropy from molecular simulations via an expansion approximation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Probability of the site juxtaposition determines the rate of protein-mediated DNA looping

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Ligand configurational entropy and protein binding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Calculation of protein-ligand binding affinities.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Chromatin structure can strongly facilitate enhancer action over a distance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Statistical-mechanical theory of DNA looping.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

A structural basis for allosteric control of DNA recombination by lambda integrase.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Calculation of absolute protein-ligand binding free energy from computer simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Simulation method for calculating the entropy and free energy of peptides and proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Entropy loss in long-distance DNA looping

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Mechanism of topology simplification by type II DNA topoisomerases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

RNA folding energy landscapes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

The topological mechanism of phage lambda integrase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4241824

7 July 2018

1 reference

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

21 January 2018

1 reference

Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

21 January 2018

1 reference

From A to B in free energy space.

21 January 2018

1 reference

A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy.

21 January 2018

1 reference

Evaluating the Accuracy of the Quasiharmonic Approximation

21 January 2018

1 reference

An efficient, path-independent method for free-energy calculations.

21 January 2018

1 reference

Simple estimation of absolute free energies for biomolecules.

21 January 2018

1 reference

Universal properties of knotted polymer rings.

21 January 2018

1 reference

Free energy of a long semiflexible polymer confined in a spherical cavity.

21 January 2018

1 reference

DNA topology and geometry in Flp and Cre recombination.

21 January 2018

1 reference

Calculation of the "absolute" free energy of a β-hairpin in an all-atom force field

21 January 2018

1 reference

Introduction to bifurcation theory

21 January 2018

1 reference

New Monte Carlo Algorithm for Protein Folding

21 January 2018

1 reference

Fluctuations of a long, semiflexible polymer in a narrow channel

21 January 2018

1 reference

12 December 2020

Stretching of semiflexible polymers with elastic bonds

1 reference

12 December 2020

Equilibrium shapes of flat knots

1 reference

12 December 2020

Equilibrium thermodynamics from basin-sampling

1 reference

12 December 2020

Multicanonical Monte Carlo simulations of a de novo designed protein with end-to-end β-sheet

1 reference

12 December 2020

Architecture of the bacteriophage T4 replication complex revealed with nanoscale biopointers

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.4900657

1 reference

3 August 2017

1 reference

1 reference

3 August 2017

1 reference