(Q42233985)

19 October 2017

Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps (English)

1 reference

19 October 2017

2

Georgios Skiniotis

1 reference

19 October 2017

Harish Vashisth

1

1 reference

PMC publication ID

3438525

19 October 2017

Charles L Brooks

series ordinal

3

1 reference

19 October 2017

1 September 2012

1 reference

19 October 2017

1 reference

19 October 2017

20

1 reference

19 October 2017

9

1 reference

19 October 2017

1453-1462

1 reference

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

19 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

ATP-Triggered Conformational Changes Delineate Substrate-Binding and -Folding Mechanics of the GroEL Chaperonin

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Parallel Generalized Born Implicit Solvent Calculations with NAMD.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Excited states of ribosome translocation revealed through integrative molecular modeling

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

The significance of G protein-coupled receptor crystallography for drug discovery

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Structural flexibility of the G alpha s alpha-helical domain in the beta2-adrenoceptor Gs complex

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Symmetry-restrained flexible fitting for symmetric EM maps

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Crystal structure of the β2 adrenergic receptor-Gs protein complex

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Stereochemical errors and their implications for molecular dynamics simulations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Molecular dynamics of EF-G during translocation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Applications of the molecular dynamics flexible fitting method

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

The role of L1 stalk-tRNA interaction in the ribosome elongation cycle

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Structure and dynamics of a processive Brownian motor: the translating ribosome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Single-particle reconstruction of biological macromolecules in electron microscopy--30 years

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Regulation of the Protein-Conducting Channel by a Bound Ribosome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Protein-induced membrane curvature investigated through molecular dynamics flexible fitting

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Scalable molecular dynamics with NAMD

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Single-particle imaging of macromolecules by cryo-electron microscopy

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

VMD: visual molecular dynamics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Classification of macromolecular assemblies studied as 'single particles'.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Conformational change of proteins arising from normal mode calculations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Single-sweep methods for free energy calculations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438525

Some recent techniques for free energy calculations

1 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22958641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Modeling Tricks and Fitting Techniques for Multiresolution Structures

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22958641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22958641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.STR.2012.08.007

1 reference

19 October 2017

1 reference

PMC publication ID

3438525

19 October 2017

PubMed publication ID

22958641

1 reference

PMC publication ID

3438525