Published in Acta Crystallogr D Biol Crystallogr on July 18, 2006
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
Features and development of Coot. Acta Crystallogr D Biol Crystallogr (2010) 89.46
The Phenix software for automated determination of macromolecular structures. Methods (2011) 3.81
Ligand identification using electron-density map correlations. Acta Crystallogr D Biol Crystallogr (2006) 2.82
Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms. Science (2016) 1.39
Structural basis of sialidase in complex with geranylated flavonoids as potent natural inhibitors. Acta Crystallogr D Biol Crystallogr (2014) 1.39
Assessment of automatic ligand building in ARP/wARP. Acta Crystallogr D Biol Crystallogr (2006) 1.38
Graphical tools for macromolecular crystallography in PHENIX. J Appl Crystallogr (2012) 1.28
Structure of catalase determined by MicroED. Elife (2014) 1.04
Vascular bioactivation of nitroglycerin by aldehyde dehydrogenase-2: reaction intermediates revealed by crystallography and mass spectrometry. J Biol Chem (2012) 0.98
Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package. Acta Crystallogr D Biol Crystallogr (2014) 0.96
Structure of the V. cholerae Na+-pumping NADH:quinone oxidoreductase. Nature (2014) 0.93
Structural basis for drug-induced allosteric changes to human β-cardiac myosin motor activity. Nat Commun (2015) 0.89
Structural Studies of Potassium Transport Protein KtrA Regulator of Conductance of K+ (RCK) C Domain in Complex with Cyclic Diadenosine Monophosphate (c-di-AMP). J Biol Chem (2015) 0.89
The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions. PLoS One (2010) 0.87
Fragmentation-tree density representation for crystallographic modelling of bound ligands. J Mol Biol (2012) 0.87
The solvent component of macromolecular crystals. Acta Crystallogr D Biol Crystallogr (2015) 0.85
Ligand placement based on prior structures: the guided ligand-replacement method. Acta Crystallogr D Biol Crystallogr (2013) 0.83
The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation. Genes Dev (2012) 0.81
Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases. J Struct Funct Genomics (2009) 0.80
McbR/YncC: implications for the mechanism of ligand and DNA binding by a bacterial GntR transcriptional regulator involved in biofilm formation. Biochemistry (2014) 0.79
Automated identification of crystallographic ligands using sparse-density representations. Acta Crystallogr D Biol Crystallogr (2014) 0.78
Elucidation of substrate specificity in Aspergillus nidulans UDP-galactose-4-epimerase. PLoS One (2013) 0.77
Mechanism of dephosphorylation of glucosyl-3-phosphoglycerate by a histidine phosphatase. J Biol Chem (2014) 0.77
The Pyruvate and α-Ketoglutarate Dehydrogenase Complexes of Pseudomonas aeruginosa Catalyze Pyocyanin and Phenazine-1-carboxylic Acid Reduction via the Subunit Dihydrolipoamide Dehydrogenase. J Biol Chem (2017) 0.75
Structures of potent anticancer compounds bound to tubulin. Protein Sci (2015) 0.75
Estimation of the protein-ligand interaction energy for model building and validation. Acta Crystallogr D Struct Biol (2017) 0.75
Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr (2013) 0.75
Ligand fitting with CCP4. Acta Crystallogr D Struct Biol (2017) 0.75
TubZ filament assembly dynamics requires the flexible C-terminal tail. Sci Rep (2017) 0.75
Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13. Cell (2017) 0.75
Crystal structure of a family 6 cellobiohydrolase from the basidiomycete Phanerochaete chrysosporium. Acta Crystallogr F Struct Biol Commun (2017) 0.75
Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) 227.01
The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr (1994) 187.88
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A (1991) 119.63
Maximum-likelihood density modification using pattern recognition of structural motifs. Acta Crystallogr D Biol Crystallogr (2001) 4.36
X-LIGAND: an application for the automated addition of flexible ligands into electron density. Acta Crystallogr D Biol Crystallogr (2001) 3.62
Modified phased translation functions and their application to molecular-fragment location. Acta Crystallogr D Biol Crystallogr (1998) 2.50
An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics (2002) 1.97
Modelling bound ligands in protein crystal structures. Acta Crystallogr D Biol Crystallogr (2004) 1.86
Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms. Chem Biol (2004) 1.80
High-throughput protein crystallography and drug discovery. Chem Soc Rev (2004) 1.46
Bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan: the structure provides further support for a rotary catalytic mechanism. Structure (1998) 1.39
Synthesis and use of iodinated nonsteroidal antiinflammatory drug analogs as crystallographic probes of the prostaglandin H2 synthase cyclooxygenase active site. Biochemistry (1996) 1.37
A new scaffold for binding haem in the cytochrome domain of the extracellular flavocytochrome cellobiose dehydrogenase. Structure (2000) 1.37
Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution. J Am Chem Soc (2003) 1.33
A rapid method for positioning small flexible molecules, nucleic acids, and large protein fragments in experimental electron density maps. Proteins (1999) 1.33
Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface. Acta Crystallogr D Biol Crystallogr (2005) 1.19
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
Phaser crystallographic software. J Appl Crystallogr (2007) 108.34
PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr (2002) 53.61
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
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D Biol Crystallogr (2009) 6.47
Recent developments in the PHENIX software for automated crystallographic structure determination. J Synchrotron Radiat (2003) 6.28
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
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
The Phenix software for automated determination of macromolecular structures. Methods (2011) 3.81
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
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
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
Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallogr D Biol Crystallogr (2012) 2.32
The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res (2008) 2.03
Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A (2005) 2.01
Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr (2010) 1.80
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
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallogr D Biol Crystallogr (2012) 1.64
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
The sequence and analysis of duplication-rich human chromosome 16. Nature (2004) 1.38
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
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
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
Coupling of receptor conformation and ligand orientation determine graded activity. Nat Chem Biol (2010) 1.25
Literature mining of protein-residue associations with graph rules learned through distant supervision. J Biomed Semantics (2012) 1.25
High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A (2003) 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
Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics (2005) 1.16
Text mining improves prediction of protein functional sites. PLoS One (2012) 1.16
Transmembrane signal transduction of the alpha(IIb)beta(3) integrin. Protein Sci (2002) 1.10
Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol (2010) 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
X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase. Structure (2003) 1.08
Improving the accuracy of macromolecular structure refinement at 7 Å resolution. Structure (2012) 1.06
Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Struct Biol (2008) 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
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. FEBS J (2014) 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
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
Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme. Rapid Commun Mass Spectrom (2012) 0.98
On the use of logarithmic scales for analysis of diffraction data. Acta Crystallogr D Biol Crystallogr (2009) 0.97
Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters. J Biol Chem (2005) 0.95
Exact direct-space asymmetric units for the 230 crystallographic space groups. Acta Crystallogr A (2011) 0.95
Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus. J Bacteriol (2005) 0.95
Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol (2010) 0.95
Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnol Bioeng (2014) 0.94
Protein structures by spallation neutron crystallography. J Synchrotron Radiat (2008) 0.94
Droplet-based microfluidic platform for heterogeneous enzymatic assays. Lab Chip (2013) 0.93
Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. Acta Crystallogr D Biol Crystallogr (2012) 0.93
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. BMC Res Notes (2012) 0.93
Biochemical and structural studies of NADH-dependent FabG used to increase the bacterial production of fatty acids under anaerobic conditions. Appl Environ Microbiol (2013) 0.92
Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front Plant Sci (2013) 0.92
Raman-spectroscopy-based noninvasive microanalysis of native lignin structure. Anal Bioanal Chem (2011) 0.92
Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels (2012) 0.91
Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. J Mol Biol (2005) 0.91