Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations (Q37008283)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18849406%20AND%20SRC:MED&resulttype=core&format=json

15 January 2020

title

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

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18849406%20AND%20SRC:MED&resulttype=core&format=json

15 January 2020

1 reference

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18849406%20AND%20SRC:MED&resulttype=core&format=json

15 January 2020

Marek Orzechowski

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15 January 2020

language of work or name

English

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publication date

10 October 2008

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15 January 2020

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15 January 2020

volume

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15 January 2020

issue

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15 January 2020

page(s)

5692-5705

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Molecular electron microscopy: state of the art and current challenges

15 January 2020

cites work

1 reference

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

29 September 2017

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Protein structure fitting and refinement guided by cryo-EM density

29 September 2017

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

29 September 2017

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

29 September 2017

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

29 September 2017

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29 September 2017

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29 September 2017

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

29 September 2017

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Structure of the E. coli protein-conducting channel bound to a translating ribosome

29 September 2017

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Simulating movement of tRNA into the ribosome during decoding

29 September 2017

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29 September 2017

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Fitting of high-resolution structures into electron microscopy reconstruction images.

29 September 2017

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Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.

29 September 2017

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Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase

29 September 2017

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

29 September 2017

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

29 September 2017

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Low-resolution structure refinement in electron microscopy.

29 September 2017

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Complementary approaches to structure determination of icosahedral viruses

29 September 2017

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Locking and unlocking of ribosomal motions

29 September 2017

1 reference

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Study of the structural dynamics of the E coli 70S ribosome using real-space refinement

29 September 2017

1 reference

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Visualizing tmRNA entry into a stalled ribosome

29 September 2017

1 reference

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A cryo-electron microscopic study of ribosome-bound termination factor RF2

29 September 2017

1 reference

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Conformational flexibility of bacterial RNA polymerase.

29 September 2017

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Using situs for flexible and rigid-body fitting of multiresolution single-molecule 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=2599853

Bridging the information gap: computational tools for intermediate resolution structure interpretation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Virus maturation involving large subunit rotations and local refolding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Steered molecular dynamics and mechanical functions 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=2599853

Three-dimensional image reconstruction of dephosphorylated smooth muscle heavy meromyosin reveals asymmetry in the interaction between myosin heads and placement of subfragment 2

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site

29 September 2017

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A dynamic model for the allosteric mechanism of GroEL

29 September 2017

1 reference

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Conformational changes studied by cryo-electron microscopy

29 September 2017

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

29 September 2017

1 reference

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

29 September 2017

1 reference

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Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch

29 September 2017

1 reference

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A database of macromolecular motions

29 September 2017

1 reference

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

29 September 2017

1 reference

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The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by 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=2599853

Conformational change of proteins arising from normal mode calculations

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Docking structures of domains into maps from cryo-electron microscopy using local correlation

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Protein flexibility predictions using graph 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=2599853

Evidence for cleft closure in actomyosin upon ADP release

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Fitting atomic models into electron-microscopy maps

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Quantitative fitting of atomic models into observed densities derived by electron microscopy.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Multi-resolution contour-based fitting of macromolecular structures

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599853

Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement

4 December 2018

1 reference

12 December 2020

Combining Electron Microscopic with X-Ray Crystallographic Structures

1 reference

12 December 2020

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

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12 December 2020

Generic rigidity percolation: The pebble game

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12 December 2020

10.1529/BIOPHYSJ.108.139451

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18849406%20AND%20SRC:MED&resulttype=core&format=json

15 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18849406%20AND%20SRC:MED&resulttype=core&format=json

15 January 2020

PubMed publication ID

18849406

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18849406%20AND%20SRC:MED&resulttype=core&format=json