Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography (Q34978052)

5 August 2017

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

1 reference

cryogenic electron microscopy

5 August 2017

X-ray crystallography

0 references

0 references

2

Elizabeth Villa

0 references

Klaus Schulten

series ordinal

5

object named as

Klaus Schulten

1 reference

5 August 2017

3

Eduard Schreiner

1 reference

5 August 2017

Leonardo G Trabuco

1

1 reference

PubMed ID

19398010

5 August 2017

Christopher B Harrison

series ordinal

4

1 reference

5 August 2017

4 May 2009

1 reference

5 August 2017

1 reference

5 August 2017

49

1 reference

5 August 2017

2

1 reference

5 August 2017

174-180

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

5 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Damped-dynamics flexible fitting

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

YUP.SCX: coaxing atomic models into medium resolution electron density maps

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Dynamics of Recognition between tRNA and elongation factor Tu

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Protein structure fitting and refinement guided by cryo-EM density

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Accelerating molecular modeling applications with graphics processors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

A structural model for the large subunit of the mammalian mitochondrial ribosome.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Scalable molecular dynamics with NAMD

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Low-resolution structure refinement in electron microscopy.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Tools for the automatic identification and classification of RNA base pairs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Using situs for flexible and rigid-body fitting of multiresolution single-molecule data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Conserved geometrical base-pairing patterns in RNA.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Situs: A package for docking crystal structures into low-resolution maps from electron microscopy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

The structure of the acto-myosin subfragment 1 complex: results of searches using data from electron microscopy and x-ray crystallography

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

VMD: visual molecular dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Real space refinement of acto-myosin structures from sectioned muscle.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2753685

Modeling Tricks and Fitting Techniques for Multiresolution Structures

26 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1016%2FJ.YMETH.2009.04.005

A short guide for molecular dynamics simulations of RNA systems.

7 January 2021

1 reference

Crossref

https://api.crossref.org/works/10.1016%2FJ.YMETH.2009.04.005

Hydrophilicity of cavities in proteins

7 January 2021

1 reference

Crossref

https://api.crossref.org/works/10.1016%2FJ.YMETH.2009.04.005

Regulation of the Protein-Conducting Channel by a Bound Ribosome

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19398010

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.YMETH.2009.04.005

1 reference

5 August 2017

1 reference

5 August 2017

1 reference

PubMed ID

19398010