Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study (Q27652286)

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Alexandre P Kuzin

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Rong Xiao

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Li-Chung Ma

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Thomas B Acton

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John F Hunt

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Michael A Kennedy

High-resolution structure prediction and the crystallographic phase problem

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language of work or name

English

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publication date

April 2009

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147-67

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cites work

1 reference

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Solution NMR structure of the barrier-to-autointegration factor-Emerin complex

20 March 2017

1 reference

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Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

20 March 2017

1 reference

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Crystal structure of the APC10/DOC1 subunit of the human anaphase-promoting complex

20 March 2017

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20 March 2017

The Protein Data Bank

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Solution structure of cyanovirin-N, a potent HIV-inactivating protein

20 March 2017

1 reference

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Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k

20 March 2017

1 reference

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Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution

20 March 2017

1 reference

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Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Human interleukin-4 and variant R88Q: phasing X-ray diffraction data by molecular replacement using X-ray and nuclear magnetic resonance models

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

The crystal structure of human endothelin

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Crystal structure of interleukin 8: symbiosis of NMR and crystallography

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Likelihood-enhanced fast translation functions

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Automated NMR structure calculation with CYANA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

The CCP4 suite: programs for protein crystallography

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Likelihood-enhanced fast rotation functions

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

The Xplor-NIH NMR molecular structure determination package

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Refinement of protein structures in explicit solvent

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Pushing the boundaries of molecular replacement with maximum likelihood

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Automated MAD and MIR structure solution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Torsion angle dynamics for NMR structure calculation with the new program Dyana

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

WHAT IF: a molecular modeling and drug design program

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Improved methods for building protein models in electron density maps and the location of errors in these models

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Free modeling with Rosetta in CASP6

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Maximum-likelihood density modification using pattern recognition of structural motifs

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Recognition of errors in three-dimensional structures of proteins

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Evaluating protein structures determined by structural genomics consortia

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

ARIA: automated NOE assignment and NMR structure calculation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

20 VERIFY3D: Assessment of protein models with three-dimensional profiles

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Physically realistic homology models built with ROSETTA can be more accurate than their templates

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

TASSER-based refinement of NMR structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

A topology-constrained distance network algorithm for protein structure determination from NOESY data.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Do all backbone polar groups in proteins form hydrogen bonds?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Protein structure estimation from minimal restraints using Rosetta.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Progress and challenges in high-resolution refinement of protein structure models.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Molecular replacement with NMR models using distance-derived pseudo B factors.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Assignment validation software suite for the evaluation and presentation of protein resonance assignment data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Theoretical and computational advances in biomolecular NMR spectroscopy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

De novo determination of protein backbone structure from residual dipolar couplings using Rosetta

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Solution solution: using NMR models for molecular replacement

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

New methods of structure refinement for macromolecular structure determination by NMR.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

The impact of direct refinement against 13C alpha and 13C beta chemical shifts on protein structure determination by NMR.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution

29 September 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878636

29 September 2017

https://api.crossref.org/works/10.1002%2FPROT.22229

Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

DRESS: a database of REfined solution NMR structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Automatic target selection for structural genomics on eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

A challenging case for protein crystal structure determination: the mating pheromone Er-1 from Euplotes raikovi

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Processing of X-ray diffraction data collected in oscillation mode

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Internal coordinates for molecular dynamics and minimization in structure determination and refinement.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

MOLREP: an Automated Program for Molecular Replacement

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

The detection of sub-units within the crystallographic asymmetric unit

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Accurate bond and angle parameters for X-ray protein structure refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Empirical Comparisons of Models for Chemical-Shift Calculation in Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

A Potential Involving Multiple Proton Chemical-Shift Restraints for Nonstereospecifically Assigned Methyl and Methylene Protons

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Improvements and Extensions in the Conformational Database Potential for the Refinement of NMR and X-ray Structures of Proteins and Nucleic Acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22229

A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited

21 January 2018

1 reference

12 December 2020

Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry

1 reference

12 December 2020

Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings

1 reference

12 December 2020

Stereochemically restrained refinement of macromolecular structures

1 reference

12 December 2020