Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics (Q29616808)

22 June 2017

title

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

1 reference

molecular dynamics simulation

22 June 2017

main subject

0 references

0 references

4

Joachim Frank

0 references

Elizabeth Villa

series ordinal

2

object named as

Elizabeth Villa

0 references

Klaus Schulten

series ordinal

5

object named as

Klaus Schulten

1 reference

22 June 2017

Leonardo G Trabuco

1

1 reference

22 June 2017

Kakoli Mitra

series ordinal

3

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=18462672

22 June 2017

language of work or name

1 reference

30 April 2017

publication date

1 May 2008

1 reference

22 June 2017

1 reference

22 June 2017

volume

16

1 reference

22 June 2017

issue

5

1 reference

22 June 2017

page(s)

673-683

1 reference

Structure of the 70S ribosome complexed with mRNA and tRNA

22 June 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Structures of the bacterial ribosome at 3.5 A resolution

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Scalable molecular dynamics with NAMD

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Tools for the automatic identification and classification of RNA base pairs

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

VMD: visual molecular dynamics

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Protein structure fitting and refinement guided by cryo-EM density

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Determining the architectures of macromolecular assemblies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Single-molecule experiments in vitro and in silico

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Molecular dynamics simulations of peptides and proteins with amplified collective motions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

From words to literature in structural proteomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Electron microscopy of functional ribosome complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Single-particle imaging of macromolecules by cryo-electron microscopy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Automated identification of filaments in cryoelectron microscopy images

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Steered molecular dynamics and mechanical functions of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Fitting atomic models into electron-microscopy maps

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Macromolecular structure determination by cryo-electron microscopy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Conserved geometrical base-pairing patterns in RNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Protein flexibility predictions using graph theory

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Evidence for cleft closure in actomyosin upon ADP release

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

The cell as a collection of protein machines: preparing the next generation of molecular biologists

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2430731

Modeling Tricks and Fitting Techniques for Multiresolution Structures

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18462672

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18462672

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The ribosome and the mechanism of protein synthesis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2008.03.005

Identifiers

DOI

10.1016/J.STR.2008.03.005

1 reference

release_c6owcmt3nbblpkwrvyi4v7u24y

22 June 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/c6owcmt3nbblpkwrvyi4v7u24y

mapped directly with Wikidata item

24 November 2022

based on heuristic

OpenCitations bibliographic resource ID

251537

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=18462672

30 April 2017

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

251537

1 reference