Published in FEBS J on June 17, 2014
A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. Acta Crystallogr D Struct Biol (2016) 0.90
A national facility for biological cryo-electron microscopy. Acta Crystallogr D Biol Crystallogr (2015) 0.89
Native proteins trap high-energy transit conformations. Sci Adv (2015) 0.82
Strategies for carbohydrate model building, refinement and validation. Acta Crystallogr D Struct Biol (2017) 0.79
An editor for the generation and customization of geometry restraints. Acta Crystallogr D Struct Biol (2017) 0.76
Conformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group. Nucleic Acids Res (2016) 0.75
Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis. Acta Crystallogr D Struct Biol (2017) 0.75
Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Crystallogr D Struct Biol (2016) 0.75
A short history of SHELX. Acta Crystallogr A (2007) 7339.18
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr (2009) 53.36
Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins (2003) 32.38
The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A (1951) 18.30
REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr (2004) 14.28
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res (2004) 9.86
Automated structure solution with the PHENIX suite. Methods Mol Biol (2008) 5.65
Stereochemically restrained refinement of macromolecular structures. Methods Enzymol (1985) 4.93
electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr D Biol Crystallogr (2009) 4.90
Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? Acta Crystallogr D Biol Crystallogr (2007) 4.51
The Phenix software for automated determination of macromolecular structures. Methods (2011) 3.81
A new generation of crystallographic validation tools for the protein data bank. Structure (2011) 3.41
Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci (1996) 2.90
Conformation dependence of backbone geometry in proteins. Structure (2009) 2.33
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallogr D Biol Crystallogr (2012) 1.64
Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values. Acta Crystallogr D Biol Crystallogr (2007) 1.62
Graphical tools for macromolecular crystallography in PHENIX. J Appl Crystallogr (2012) 1.28
Numerology versus reality: a voice in a recent dispute. Acta Crystallogr D Biol Crystallogr (2007) 1.26
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A (2011) 1.23
Comment on Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? by Jaskolski, Gilski, Dauter & Wlodawer (2007). Acta Crystallogr D Biol Crystallogr (2007) 1.20
Relaxation of backbone bond geometry improves protein energy landscape modeling. Protein Sci (2014) 1.19
Full-matrix refinement of the protein crambin at 0.83 A and 130 K. Acta Crystallogr D Biol Crystallogr (1995) 1.18
Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. Acta Crystallogr D Biol Crystallogr (2010) 1.17
The flexibility in the proline ring couples to the protein backbone. Protein Sci (2005) 1.12
On the complexity of Engh and Huber refinement restraints: the angle τ as example. Acta Crystallogr D Biol Crystallogr (2010) 1.10
A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallogr D Biol Crystallogr (2008) 1.05
A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution. Acta Crystallogr D Biol Crystallogr (2011) 1.05
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Crystallogr D Biol Crystallogr (2012) 1.00
Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. Nucleic Acids Res (2009) 0.99
Model-building strategies for low-resolution X-ray crystallographic data. Acta Crystallogr D Biol Crystallogr (2009) 0.96
Proteins do not have strong spines after all. Structure (2009) 0.94
Interplay between peptide bond geometrical parameters in nonglobular structural contexts. Biomed Res Int (2013) 0.83
Structural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein. Acta Crystallogr D Biol Crystallogr (1998) 0.81
Phaser crystallographic software. J Appl Crystallogr (2007) 108.34
Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr (2012) 11.31
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr (2007) 7.72
Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling. Science (2003) 6.96
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D Biol Crystallogr (2009) 6.47
Structural basis for double-stranded RNA processing by Dicer. Science (2006) 5.86
Automated structure solution with the PHENIX suite. Methods Mol Biol (2008) 5.65
Automated ligand fitting by core-fragment fitting and extension into density. Acta Crystallogr D Biol Crystallogr (2006) 5.03
electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr D Biol Crystallogr (2009) 4.90
A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr D Biol Crystallogr (2005) 4.82
SPARX, a new environment for Cryo-EM image processing. J Struct Biol (2006) 4.66
Surprises and pitfalls arising from (pseudo)symmetry. Acta Crystallogr D Biol Crystallogr (2007) 4.44
Averaged kick maps: less noise, more signal... and probably less bias. Acta Crystallogr D Biol Crystallogr (2009) 3.62
Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science (2013) 3.60
Protein sulfenic acids in redox signaling. Annu Rev Pharmacol Toxicol (2004) 3.56
Robust indexing for automatic data collection. J Appl Crystallogr (2004) 3.51
A new generation of crystallographic validation tools for the protein data bank. Structure (2011) 3.41
Crystallographic model quality at a glance. Acta Crystallogr D Biol Crystallogr (2009) 3.11
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Crystallogr D Biol Crystallogr (2008) 3.07
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Crystallogr D Biol Crystallogr (2007) 3.07
Ligand identification using electron-density map correlations. Acta Crystallogr D Biol Crystallogr (2006) 2.82
On macromolecular refinement at subatomic resolution with interatomic scatterers. Acta Crystallogr D Biol Crystallogr (2007) 2.75
A novel mechanism of chemoprotection by sulforaphane: inhibition of histone deacetylase. Cancer Res (2004) 2.71
Automatic multiple-zone rigid-body refinement with a large convergence radius. J Appl Crystallogr (2009) 2.66
Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proc Natl Acad Sci U S A (2012) 2.43
Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredoxins. Biochemistry (2002) 2.41
Conformation dependence of backbone geometry in proteins. Structure (2009) 2.33
Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallogr D Biol Crystallogr (2012) 2.32
Crystal structure of mammalian cysteine dioxygenase. A novel mononuclear iron center for cysteine thiol oxidation. J Biol Chem (2006) 2.30
A putative Fe2+-bound persulfenate intermediate in cysteine dioxygenase. Biochemistry (2008) 2.09
The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res (2008) 2.03
Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin. Biochemistry (2005) 2.01
Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A (2005) 2.01
Lessons from the lysozyme of phage T4. Protein Sci (2010) 1.85
Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr (2010) 1.80
Structure-based insights into the catalytic power and conformational dexterity of peroxiredoxins. Antioxid Redox Signal (2011) 1.79
Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. EMBO J (2003) 1.78
Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production. Structure (2011) 1.67
Self-masking in an intact ERM-merlin protein: an active role for the central alpha-helical domain. J Mol Biol (2006) 1.66
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallogr D Biol Crystallogr (2012) 1.64
Substrate specificity and redox potential of AhpC, a bacterial peroxiredoxin. Proc Natl Acad Sci U S A (2007) 1.62
Cysteine-based redox switches in enzymes. Antioxid Redox Signal (2010) 1.62
Modelling dynamics in protein crystal structures by ensemble refinement. Elife (2012) 1.62
Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J Mol Biol (2004) 1.56
Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc Natl Acad Sci U S A (2005) 1.54
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J Struct Funct Genomics (2012) 1.53
Structural evidence that peroxiredoxin catalytic power is based on transition-state stabilization. J Mol Biol (2010) 1.46
Cysteine pK(a) values for the bacterial peroxiredoxin AhpC. Biochemistry (2008) 1.42
Structure of the active N-terminal domain of Ezrin. Conformational and mobility changes identify keystone interactions. J Biol Chem (2002) 1.41
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics (2011) 1.36
Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. Proc Natl Acad Sci U S A (2012) 1.33
Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality. J Mol Biol (2010) 1.33
The EBP50-moesin interaction involves a binding site regulated by direct masking on the FERM domain. J Cell Sci (2004) 1.31
Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production. Metab Eng (2013) 1.31
Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng (2012) 1.30
Molecular dynamics applied to X-ray structure refinement. Acc Chem Res (2002) 1.30
Targeted proteomics for metabolic pathway optimization: application to terpene production. Metab Eng (2011) 1.29
Graphical tools for macromolecular crystallography in PHENIX. J Appl Crystallogr (2012) 1.28
Structure and dynamics of LC8 complexes with KXTQT-motif peptides: swallow and dynein intermediate chain compete for a common site. J Mol Biol (2007) 1.27
Crystal structure of a novel Plasmodium falciparum 1-Cys peroxiredoxin. J Mol Biol (2005) 1.27
Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol (2013) 1.27
Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J Biol Chem (2010) 1.26
Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nat Methods (2013) 1.26
Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS. J Mol Biol (2007) 1.26
Coupling of receptor conformation and ligand orientation determine graded activity. Nat Chem Biol (2010) 1.25
High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A (2003) 1.23
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A (2011) 1.23
Phaser.MRage: automated molecular replacement. Acta Crystallogr D Biol Crystallogr (2013) 1.20
Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface. Acta Crystallogr D Biol Crystallogr (2005) 1.19
Automatic solution of heavy-atom substructures. Methods Enzymol (2003) 1.18
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J Appl Crystallogr (2010) 1.18
Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. Acta Crystallogr D Biol Crystallogr (2010) 1.17
Identification and characterization of bacterial cysteine dioxygenases: a new route of cysteine degradation for eubacteria. J Bacteriol (2006) 1.16
Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics (2005) 1.16
Catalytic cycle of human glutathione reductase near 1 A resolution. J Mol Biol (2008) 1.16
Crystal structure of the antioxidant enzyme glutathione reductase inactivated by peroxynitrite. J Biol Chem (2001) 1.14
Structural changes common to catalysis in the Tpx peroxiredoxin subfamily. J Mol Biol (2009) 1.12
Transmembrane signal transduction of the alpha(IIb)beta(3) integrin. Protein Sci (2002) 1.10
Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc Natl Acad Sci U S A (2013) 1.10
Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol (2010) 1.10
Structure of Ptr ToxA: an RGD-containing host-selective toxin from Pyrenophora tritici-repentis. Plant Cell (2005) 1.09
X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase. Structure (2003) 1.08
Oxidized and synchrotron cleaved structures of the disulfide redox center in the N-terminal domain of Salmonella typhimurium AhpF. Protein Sci (2005) 1.08
Multivalency in the assembly of intrinsically disordered Dynein intermediate chain. J Biol Chem (2009) 1.08
Improving the accuracy of macromolecular structure refinement at 7 Å resolution. Structure (2012) 1.06
Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. J Mol Biol (2004) 1.05
A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallogr D Biol Crystallogr (2008) 1.05
On the occurrence of linear groups in proteins. Protein Sci (2009) 1.05
A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution. Acta Crystallogr D Biol Crystallogr (2011) 1.05
The Arg-Gly-Asp-containing, solvent-exposed loop of Ptr ToxA is required for internalization. Mol Plant Microbe Interact (2008) 1.03
Tuning of peroxiredoxin catalysis for various physiological roles. Biochemistry (2014) 1.02
Peroxiredoxins in parasites. Antioxid Redox Signal (2012) 1.01
A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. Biomol Concepts (2010) 1.01
Intensity statistics in the presence of translational noncrystallographic symmetry. Acta Crystallogr D Biol Crystallogr (2013) 1.01
The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. J Struct Funct Genomics (2012) 1.00
The crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly. J Biol Chem (2010) 1.00
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Crystallogr D Biol Crystallogr (2012) 1.00
Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. ACS Chem Biol (2008) 0.99
The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8. J Mol Biol (2008) 0.99
Iron-containing urease in a pathogenic bacterium. Proc Natl Acad Sci U S A (2011) 0.99