(Q41839184)

English

Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

scientific article published on 17 July 2012

In more languages

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. (English)

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

crystal structure

1 reference

based on heuristic

inferred from title

author name string

Jeffrey A Bell

1

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Kenneth L Ho

2

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Ramy Farid

3

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

language of work or name

1 reference

based on heuristic

inferred from title

publication date

17 July 2012

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Acta Crystallographica Section D: Biological Crystallography

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

68

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Pt 8

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

935-952

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals

1 reference

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Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Refinement of protein structures in explicit solvent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

The Refined Crystal Structure of an Eel Pout Type III Antifreeze Protein RD1 at 0.62-Å Resolution Reveals Structural Microheterogeneity of Protein and Solvation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

The Cambridge Structural Database: a quarter of a million crystal structures and rising

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Packed protein bilayers in the 0.90 å resolution structure of a designed alpha helical bundle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Deviations from planarity of the peptide bond in peptides and proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Errors in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Refinement of the influenza virus hemagglutinin by simulated annealing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

6 June 2018

Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

Polarizable atomic multipole X-ray refinement: weighting schemes for macromolecular diffraction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

Elucidation of the phosphate binding mode of DING proteins revealed by subangstrom X-ray crystallography.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

Atomic resolution structures and solution behavior of enzyme-substrate complexes of Enterobacter cloacae PB2 pentaerythritol tetranitrate reductase. Multiple conformational states and implications for the mechanism of nitroaromatic explosive degrada

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413210

18 August 2018

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

van der Waals Volumes and Radii

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

FYX-051: a novel and potent hybrid-type inhibitor of xanthine oxidoreductase

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Reverse type I inhibitor of Mycobacterium tuberculosis CYP125A1

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Validation of protein structures derived by NMR spectroscopy

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Improved Fourier coefficients for maps using phases from partial structures with errors

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

1 reference

https://api.crossref.org/works/10.1107%2FS0907444912017453

21 January 2018

Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Eucommia ulmoides Oliver at an atomic resolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/22868759

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S

1 reference

https://pubmed.ncbi.nlm.nih.gov/22868759

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydrophobin HFBII in detail: ultrahigh-resolution structure at 0.75 Å

1 reference

https://pubmed.ncbi.nlm.nih.gov/22868759

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stereochemically restrained refinement of macromolecular structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/22868759

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1107/S0907444912017453

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

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