Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution (Q36404096)

14 August 2017

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

1 reference

14 August 2017

2

1 reference

14 August 2017

Gunnar F Schröder

1

0 references

Michael Levitt

series ordinal

3

object named as

Michael Levitt

1 reference

PMC publication ID

2213367

14 August 2017

language of work or name

1 reference

1 December 2007

1 reference

14 August 2017

1 reference

14 August 2017

15

1 reference

14 August 2017

12

1 reference

14 August 2017

1630-1641

1 reference

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Crystallographic R factor refinement by molecular dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Visualizing density maps with UCSF Chimera

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Combining X-ray crystallography and electron microscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Assessment of phase accuracy by cross validation: the free R value. Methods and applications

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Low-resolution structure refinement in electron microscopy.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Multiple open forms of ribose-binding protein trace the path of its conformational change

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Refinement of protein dynamic structure: normal mode refinement

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Fast 3D motif search of EM density maps using a locally normalized cross-correlation function

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

On the potential of normal-mode analysis for solving difficult molecular-replacement problems

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Fitting atomic models into electron-microscopy maps

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Prediction of protein conformational freedom from distance constraints

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Considerations for the refinement of low-resolution crystal structures

21 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Low-Resolution Crystallography Is Coming of Age

5 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

Multi-resolution contour-based fitting of macromolecular structures

5 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

5 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2213367

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

5 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18073112

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Real-space molecular-dynamics structure refinement

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18073112

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Topology representing neural networks reconcile biomolecular shape, structure, and dynamics

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2007.09.021

PROCHECK: a program to check the stereochemical quality of protein structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2007.09.021

Identifiers

DOI

10.1016/J.STR.2007.09.021

1 reference

14 August 2017

1 reference

PMC publication ID

2213367

14 August 2017

PubMed publication ID

18073112

1 reference

PMC publication ID

2213367