Electron density server at Uppsala university
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A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are provided for assessing the goodness-of-fit between the deposited models (structures) and the experimental data represented by the electron density calculated using the models and their associated structure factor amplitudes.
Description
More detailed information about this field from each metasource.
A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are provided for assessing the goodness-of-fit between the deposited models (structures) and the experimental data represented by the electron density calculated using the models and their associated structure factor amplitudes.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:41.578991
Webpage:
http://eds.bmc.uu.se/eds/Webpage
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
The Uppsala Electron-Density Server
PMID: 15572777
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:41.578991
Publications
More detailed information about this field from each metasource.
The Uppsala Electron-Density Server
PMID: 15572777
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:41.578991
-
The Uppsala Electron-Density Server
PubMed citations: 181.
181 articles citing: The Uppsala Electron-Density Server
Disruption of Claudin-Made Tight Junction Barriers by Clostridium perfringens Enterotoxin: Insights from Structural Biology. PMID:35269525
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant. PMID:34929737
The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. PMID:34779043
Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells. PMID:34696326
Ankyrin repeats in context with human population variation. PMID:34428215
Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones. PMID:34352093
Mapping the multiscale structure of biological systems. PMID:34139169
The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation. PMID:33888588
Comment on "Structural evidence for a dynamic metallocofactor during N2 reduction by Mo-nitrogenase". PMID:33574183
Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase. PMID:33574035
A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins. PMID:33559613
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. PMID:33404525
Interaction of the pioneer transcription factor GATA3 with nucleosomes. PMID:32811816
A chemical interpretation of protein electron density maps in the worldwide protein data bank. PMID:32785279
The data universe of structural biology. PMID:32695409
Nucleosome binding by the pioneer transcription factor OCT4. PMID:32678275
Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy. PMID:32231015
Computational reconstruction of atomistic protein structures from coarse-grained models. PMID:31969975
Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics. PMID:31910338
Factors influencing estimates of coordinate error for molecular replacement. PMID:31909740
Common activation mechanism of class A GPCRs. PMID:31855179
Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank. PMID:31480623
A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. PMID:31390767
Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding. PMID:31069272
A close look onto structural models and primary ligands of metallo-β-lactamases. PMID:30466711
Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 Å resolution. PMID:30333622
Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein. PMID:30226758
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Structural analysis of glycoproteins: building N-linked glycans with Coot. PMID:29652253
Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence. PMID:29563192
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Validation of ligands in macromolecular structures determined by X-ray crystallography. PMID:29533230
An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains. PMID:29518032
Validation of Structures in the Protein Data Bank. PMID:29174494
Detect, correct, retract: How to manage incorrect structural models. PMID:29113027
MolProbity: More and better reference data for improved all-atom structure validation. PMID:29067766
A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. PMID:29057824
A distance geometry-based description and validation of protein main-chain conformation. PMID:28989721
Mechanism of Rv2837c from Mycobacterium tuberculosis remains controversial. PMID:28801352
Molden 2.0: quantum chemistry meets proteins. PMID:28752344
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Stereochemistry and Validation of Macromolecular Structures. PMID:28573590
Twilight reloaded: the peptide experience. PMID:28291756
Estimation of the protein-ligand interaction energy for model building and validation. PMID:28291754
Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1. PMID:28258219
Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive. PMID:28216043
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
The young person's guide to the PDB. PMID:28132477
Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors. PMID:28108896
When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode? PMID:27982595
Mg2+ ions: do they bind to nucleobase nitrogens? PMID:27923930
A public database of macromolecular diffraction experiments. PMID:27841751
Simplifying and enhancing the use of PyMOL with horizontal scripts. PMID:27488983
Crystal structure of the cyan fluorescent protein Cerulean-S175G. PMID:27380368
Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource. PMID:27345761
DCC: a Swiss army knife for structure factor analysis and validation. PMID:27275151
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. PMID:27139625
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. PMID:27050687
Molprobity's ultimate rotamer-library distributions for model validation. PMID:27018641
Allosteric switch regulates protein-protein binding through collective motion. PMID:26961002
Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites. PMID:26914344
First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer. PMID:26884182
Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism. PMID:26776105
Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. PMID:26628682
Differential Regulation of 6- and 7-Transmembrane Helix Variants of μ-Opioid Receptor in Response to Morphine Stimulation. PMID:26554831
Towards predictive docking at aminergic G-protein coupled receptors. PMID:26453085
Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA. PMID:26358812
Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. PMID:26327386
Detection of trans-cis flips and peptide-plane flips in protein structures. PMID:26249342
The solvent component of macromolecular crystals. PMID:25945568
Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps. PMID:25760616
Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol. PMID:25760593
Models of protein-ligand crystal structures: trust, but verify. PMID:25665575
The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis. PMID:25664789
Three-dimensional structures of laccases. PMID:25586561
The multifaceted subunit interfaces of ionotropic glutamate receptors. PMID:25556789
You are lost without a map: Navigating the sea of protein structures. PMID:25554228
Small molecule annotation for the Protein Data Bank. PMID:25425036
Metrics for comparison of crystallographic maps. PMID:25286844
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. PMID:25286839
Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. PMID:25075337
Automated identification of crystallographic ligands using sparse-density representations. PMID:25004962
Theoretical insight into the mechanism for the inhibition of the cysteine protease cathepsin B by 1,2,4-thiadiazole derivatives. PMID:24881000
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. PMID:24848013
Anomalies in the refinement of isoleucine. PMID:24699648
Lysine carboxylation: unveiling a spontaneous post-translational modification. PMID:24419378
Two high-resolution structures of the human E3 ubiquitin ligase Siah1. PMID:24316825
RNA Bricks--a database of RNA 3D motifs and their interactions. PMID:24220091
Modelling three-dimensional protein structures for applications in drug design. PMID:24216321
SCEDS: protein fragments for molecular replacement in Phaser. PMID:24189233
An analysis of oligomerization interfaces in transmembrane proteins. PMID:24134166
Unexpected features in the Protein Data Bank entries 3qd1 and 4i8e: the structural description of the binding of the serine-rich repeat adhesin GspB to host cell carbohydrate receptor is not a solved issue. PMID:24100551
Crystallographic model validation: from diagnosis to healing. PMID:24064406
The crystal structure of an extracellular catechol oxidase from the ascomycete fungus Aspergillus oryzae. PMID:24043469
Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. PMID:24034303
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. PMID:23895374
Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. PMID:23814507
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. PMID:23617227
CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. PMID:23548044
Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach. PMID:23519660
Transmembrane signaling and assembly of the cytochrome b6f-lipidic charge transfer complex. PMID:23507619
Linking receptor activation to changes in Sw I and II of Gα proteins. PMID:23466875
Visualizing ligand molecules in Twilight electron density. PMID:23385767
Improving protocols for protein mapping through proper comparison to crystallography data. PMID:23327200
PubChem3D: conformer ensemble accuracy. PMID:23289532
Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation. PMID:23226391
Structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in RNA crystal structures. PMID:23152878
Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (part I): virtual screening and activity assays. PMID:22984596
Computational prediction of N-linked glycosylation incorporating structural properties and patterns. PMID:22782545
Aromatic residues in the substrate cleft of RPE65 protein govern retinol isomerization and modulate its progression. PMID:22745121
Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. PMID:22696403
Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen. PMID:22505400
PDB_REDO: constructive validation, more than just looking for errors. PMID:22505269
Implementing an X-ray validation pipeline for the Protein Data Bank. PMID:22505268
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. PMID:22505257
Unusual arginine formations in protein function and assembly: rings, strings, and stacks. PMID:22497303
PDB_REDO: automated re-refinement of X-ray structure models in the PDB. PMID:22477769
Fragmentation-tree density representation for crystallographic modelling of bound ligands. PMID:22446381
Crystallographic analysis of small ribozymes and riboswitches. PMID:22315069
PDB ligand conformational energies calculated quantum-mechanically. PMID:22303903
The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures. PMID:22246295
Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B). PMID:22169623
Crystal structure of the Japanese encephalitis virus envelope protein. PMID:22156523
Improving molecular docking through eHiTS' tunable scoring function. PMID:22076470
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. PMID:22034521
A new generation of crystallographic validation tools for the protein data bank. PMID:22000512
Crystal structure of Onconase at 1.1 Å resolution--insights into substrate binding and collective motion. PMID:21895975
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. PMID:21645855
The role of Co²+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols. PMID:21505236
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
ePMV embeds molecular modeling into professional animation software environments. PMID:21397181
Protein structure reports in JIMD--an important enhancement of journal scope. PMID:21369958
Protein structure databases. PMID:21225378
The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease. PMID:21177854
The binding interface of cytochrome c and cytochrome c₁ in the bc₁ complex: rationalizing the role of key residues. PMID:20959106
Interactions of cytochrome P450s with their ligands. PMID:20939998
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. PMID:20648263
Automated electron-density sampling reveals widespread conformational polymorphism in proteins. PMID:20499387
Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PMID:20442867
Detection of unrealistic molecular environments in protein structures based on expected electron densities. PMID:20405167
Features and development of Coot. PMID:20383002
Visualization of macromolecular structures. PMID:20195256
Practical application of bioinformatics by the multidisciplinary VIZIER consortium. PMID:20153379
QM/MM X-ray refinement of zinc metalloenzymes. PMID:20116858
MolProbity: all-atom structure validation for macromolecular crystallography. PMID:20057044
Recipes for the selection of experimental protein conformations for virtual screening. PMID:20000587
PDBe: Protein Data Bank in Europe. PMID:19858099
A new method for publishing three-dimensional content. PMID:19841676
Crystal structure and catalytic mechanism of 4-methylmuconolactone methylisomerase. PMID:19801657
The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. PMID:19731372
The flexible pocketome engine for structural chemogenomics. PMID:19727619
Homology modelling and spectroscopy, a never-ending love story. PMID:19718498
Recent developments in phasing and structure refinement for macromolecular crystallography. PMID:19700309
Averaged kick maps: less noise, more signal... and probably less bias. PMID:19690370
Improved prediction of protein side-chain conformations with SCWRL4. PMID:19603484
Operator-assisted harvesting of protein crystals using a universal micromanipulation robot. PMID:19461845
An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. PMID:19173308
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. PMID:19171973
Case-controlled structure validation. PMID:19171969
On vital aid: the why, what and how of validation. PMID:19171968
Crystal structure of Streptococcus pyogenes sortase A: implications for sortase mechanism. PMID:19129180
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. PMID:19090659
Data deposition and annotation at the worldwide protein data bank. PMID:19082769
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. PMID:19053777
Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase. PMID:18940872
Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms. PMID:18840291
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. PMID:18453687
Remediation of the protein data bank archive. PMID:18073189
Structure of PlcR: Insights into virulence regulation and evolution of quorum sensing in Gram-positive bacteria. PMID:17998541
Cloning, expression, purification, crystallization and preliminary X-ray analysis of Thermus aquaticus succinyl-CoA synthetase. PMID:17565180
Predicting helical coaxial stacking in RNA multibranch loops. PMID:17507661
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. PMID:17452350
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. PMID:17401565
Assessment of automatic ligand building in ARP/wARP. PMID:17164533
Crystallographic refinement of ligand complexes. PMID:17164531
E-MSD: improving data deposition and structure quality. PMID:16381867
Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights. PMID:16027359
A test of enhancing model accuracy in high-throughput crystallography. PMID:15965733
Do all backbone polar groups in proteins form hydrogen bonds? PMID:15937286
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