Can morphing methods predict intermediate structures? (Q30373205)

19 August 2017

Can morphing methods predict intermediate structures? (English)

1 reference

19 August 2017

Michael Levitt

1 reference

19 August 2017

Dahlia R Weiss

1 reference

PMC publication ID

2691871

19 August 2017

language of work or name

English

0 references

publication date

30 October 2008

1 reference

Journal of Molecular Biology

19 August 2017

1 reference

19 August 2017

385

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19 August 2017

1 reference

19 August 2017

665-674

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

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

A natural coarse graining for simulating large biomolecular motion

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

The Database of Macromolecular Motions: new features added at the decade mark

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Intermediate states of ribonuclease III in complex with double-stranded RNA.

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Structural mechanism of the recovery stroke in the myosin molecular motor

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Long-timescale simulation methods

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Normal-modes-based prediction of protein conformational changes guided by distance constraints

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Use of non-crystallographic symmetry in protein structure refinement

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Trapping a 96 degrees domain rotation in two distinct conformations by engineered disulfide bridges

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

FATCAT: a web server for flexible structure comparison and structure similarity searching

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Crystal structure of scallop Myosin s1 in the pre-power stroke state to 2.6 a resolution: flexibility and function in the head

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Efficient generation of feasible pathways for protein conformational transitions

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Structural changes in the calcium pump accompanying the dissociation of calcium

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

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

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Visualizing protein conformational changes on a personal computer--alpha carbon pseudo bonding as a constraint for interpolation in internal coordinate space

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Conformational change of proteins arising from normal mode calculations

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Three conformational states of scallop myosin S1

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

A database of macromolecular motions

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

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

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

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

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

The T<-->R structural transition of insulin; pathways suggested by targeted energy minimization

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Protein folding by motion planning

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Crystal structure of the calcium pump with a bound ATP analogue

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691871

Elastic models of conformational transitions in macromolecules

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18996395

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

String method for the study of rare events

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2008.10.064

Identifiers

DOI

10.1016/J.JMB.2008.10.064

1 reference

19 August 2017

1 reference

PMC publication ID

2691871

19 August 2017

PubMed publication ID

18996395

1 reference

PMC publication ID

2691871