Towards automated crystallographic structure refinement with phenix.refine (Q27860678)

10

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Thomas C. Terwilliger

7

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Ralf W Grosse-Kunstleve

2

Ralf W Grosse-Kunstleve

0 references

Alexandre Urzhumtsev

8

Alexandre Urzhumtsev

0 references

Pavel V Afonine

1

Pavel V Afonine

0 references

Jeffrey J Headd

4

Jeffrey J Headd

0 references

Peter H. Zwart

9

Peter H Zwart

0 references

Nigel W Moriarty

5

Nigel W Moriarty

0 references

Marat Mustyakimov

6

Acta Crystallographica Section D: Biological Crystallography

Marat Mustyakimov

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publication date

April 2012

0 references

published in

0 references

volume

68

0 references

page(s)

352-67

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issue

Pt 4

0 references

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Crystal structure of the GluR2 amino-terminal domain provides insights into the architecture and assembly of ionotropic glutamate receptors

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Efalizumab binding to the LFA-1 L I domain blocks ICAM-1 binding via steric hindrance

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

20 March 2017

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Mechanism of activation and inhibition of the HER4/ErbB4 kinase

20 March 2017

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A short history of SHELX

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Version 1.2 of the Crystallography and NMR system

20 March 2017

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Crystallographic R factor refinement by molecular dynamics

20 March 2017

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The rare crystallographic structure of d(CGCGCG)(2): the natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)(2) at 10 degrees C

20 March 2017

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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

20 March 2017

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Crystal Structures of the Pilus Retraction Motor PilT Suggest Large Domain Movements and Subunit Cooperation Drive Motility

20 March 2017

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Optimal description of a protein structure in terms of multiple groups undergoing TLS motion

20 March 2017

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REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

20 March 2017

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Coot: model-building tools for molecular graphics

20 March 2017

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Refinement of macromolecular structures by the maximum-likelihood method

20 March 2017

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PHENIX: building new software for automated crystallographic structure determination

20 March 2017

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Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 Å resolution

20 March 2017

1 reference

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Crystal structure of the human CD4 N-terminal two-domain fragment complexed to a class II MHC molecule

20 March 2017

1 reference

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Use of TLS parameters to model anisotropic displacements in macromolecular refinement

20 March 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

20 March 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

High-resolution structure of the HNF-1alpha dimerization domain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography

20 March 2017

1 reference

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Crystal structure of cathepsin X: a flip-flop of the ring of His23 allows carboxy-monopeptidase and carboxy-dipeptidase activity of the protease

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Crystal structure of the cytosolic C2A-C2B domains of synaptotagmin III. Implications for Ca(+2)-independent snare complex interaction

20 March 2017

1 reference

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1.7 A structure of the stabilized REIv mutant T39K. Application of local NCS restraints

20 March 2017

1 reference

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

20 March 2017

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Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution

20 March 2017

1 reference

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Structure and refinement of oxymyoglobin at 1.6 A resolution

20 March 2017

1 reference

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

20 March 2017

1 reference

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The Protein Data Bank: a computer-based archival file for macromolecular structures

20 March 2017

1 reference

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Use of non-crystallographic symmetry in protein structure refinement

20 March 2017

1 reference

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Structure of C3b reveals conformational changes that underlie complement activity

20 March 2017

1 reference

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Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement

20 March 2017

1 reference

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electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation

20 March 2017

1 reference

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Incorporation of prior phase information strengthens maximum-likelihood structure refinement

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Joint X-ray and neutron refinement with phenix.refine

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

On the use of logarithmic scales for analysis of diffraction data

29 September 2017

1 reference

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Averaged kick maps: less noise, more signal... and probably less bias

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Automatic multiple-zone rigid-body refinement with a large convergence radius

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules

29 September 2017

1 reference

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Crystallographic model quality at a glance

29 September 2017

1 reference

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X-ray structure determination at low resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular 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=3322595

Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Molecular dynamics applied to X-ray structure refinement

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Detecting outliers in non-redundant diffraction 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=3322595

Experimental assessment of differences between related 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=3322595

Proteins at atomic resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Where freedom is given, liberties are taken

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Structural models of human apolipoprotein A-I.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

On the derivation of dynamic information from diffraction 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=3322595

Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

The benefits of atomic resolution.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Exact direct-space asymmetric units for the 230 crystallographic space groups.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Considerations for the refinement of low-resolution crystal structures

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Crystal structure of a Cbtx-AChBP complex reveals essential interactions between snake alpha-neurotoxins and nicotinic receptors.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

On a fast calculation of structure factors at a subatomic resolution.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

27 November 2018

Introduction to twinning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Simulated-annealing real-space refinement as a tool in model building.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Likelihood-based refinement. I. Irremovable model errors.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

High-resolution neutron structure of nicotinamide adenine dinucleotide

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322595

Flat bulk-solvent model: obtaining optimal parameters

27 November 2018

1 reference

12 December 2020

The Bijvoet-difference Fourier synthesis

1 reference

12 December 2020

A robust bulk-solvent correction and anisotropic scaling procedure

1 reference

12 December 2020

On macromolecular refinement at subatomic resolution with interatomic scatterers

1 reference

12 December 2020

Processing of X-ray diffraction data collected in oscillation mode

1 reference

12 December 2020

Stereochemically restrained refinement of macromolecular structures

1 reference

12 December 2020

Experience with various techniques for the refinement of protein structures

1 reference

12 December 2020

TNT refinement package

1 reference

12 December 2020