Protein structure determination by combining sparse NMR data with evolutionary couplings (Q28914765)

4

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Debora Marks

5

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Gaetano T. Montelione

6

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Thomas A Hopf

3

object named as

Thomas A Hopf

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author name string

Yuefeng Tang

1

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Yuanpeng Janet Huang

Sequence co-evolution gives 3D contacts and structures of protein complexes

2

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language of work or name

English

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publication date

August 2015

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published in

Nature Methods

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volume

12

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page(s)

751-4

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issue

8

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cites work

1 reference

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16 March 2017

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PDBStat: a universal restraint converter and restraint analysis software package for protein NMR

16 March 2017

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Protein structure prediction from sequence variation

16 March 2017

1 reference

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The program XEASY for computer-supported NMR spectral analysis of biological macromolecules

16 March 2017

1 reference

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Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

16 March 2017

1 reference

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Three-dimensional structures of membrane proteins from genomic sequencing

16 March 2017

1 reference

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Protein 3D structure computed from evolutionary sequence variation

16 March 2017

1 reference

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Direct-coupling analysis of residue coevolution captures native contacts across many protein families

16 March 2017

1 reference

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NMR structure determination for larger proteins using backbone-only data

16 March 2017

1 reference

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TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

16 March 2017

1 reference

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Solution Structure of the Integral Human Membrane Protein VDAC-1 in Detergent Micelles

16 March 2017

1 reference

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Consistent blind protein structure generation from NMR chemical shift data

16 March 2017

1 reference

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Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

16 March 2017

1 reference

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Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein

16 March 2017

1 reference

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MOLMOL: a program for display and analysis of macromolecular structures

16 March 2017

1 reference

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Main-chain bond lengths and bond angles in protein structures

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Recognition of errors in three-dimensional structures of proteins

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Assessment of protein models with three-dimensional profiles

16 March 2017

1 reference

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Accelerated Profile HMM Searches

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Evaluating protein structures determined by structural genomics consortia

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

7 April 2017

1 reference

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Protein structure prediction using Rosetta

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal 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=4521990

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Emerging methods in protein co-evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Deuterium isotope shifts for backbone ¹H, ¹⁵N and ¹³C nuclei in intrinsically disordered protein α-synuclein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Genomics-aided structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

RPF: a quality assessment tool for protein NMR 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=4521990

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Improved technologies now routinely provide protein NMR structures useful for molecular replacement

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Preparation of protein samples for NMR structure, function, and small-molecule screening studies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Optimal isotope labelling for NMR protein structure determinations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

A topology-constrained distance network algorithm for protein structure determination from NOESY 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=4521990

An integrated platform for automated analysis of protein NMR 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=4521990

Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Solution NMR-derived global fold of a monomeric 82-kDa enzyme

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Automated analysis of protein NMR assignments and 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=4521990

Residual dipolar couplings in structure determination of biomolecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

Weak alignment offers new NMR opportunities to study protein structure and 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=4521990

Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4521990

An efficient strategy for assignment of cross-peaks in 3D heteronuclear NOESY experiments.

3 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3455

REDCAT: a residual dipolar coupling analysis tool.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3455

Global Folds of Highly Deuterated, Methyl-Protonated Proteins by Multidimensional NMR†

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3455

Selective Methyl Group Protonation of Perdeuterated Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3455

Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26121406

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NMETH.3455

1 reference

Dimensions Publication ID

1697591

1025522845

0 references

1697591

1 reference

1 reference

1 reference