PDB-REDO

Names
More detailed information about this field from each metasource.

PDB-REDO
metasource: Fairsharing.org
version: None

PDB-REDO databank of optimised macromolecular structures
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

pdb-redo
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

Other names: PDB-REDO databank of optimised macromolecular structures, pdb-redo

PDB-REDO is a databank of optimised (re-refined, rebuilt and validated) Protein Data Bank entries. It covers nearly all structure models derived from X-ray and electron diffraction that have deposited experimental data. Entries can be accessed by their PDB identifier.

Webpage:

https://pdb-redo.eu

Licence:

Name: PDB-REDO Licence
URL: https://pdb-redo.eu/license.txt

Publications: (11)

Publications
More detailed information about this field from each metasource.

A series of PDB related databases for everyday needs
PMID: 21071423
metasource: Fairsharing.org
version: None

PDB_REDO: automated re-refinement of X-ray structure models in the PDB
PMID: 22477769
metasource: Fairsharing.org
version: None

http://dx.doi.org/10.1107/S0907444911054515
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1107/S0021889809008784
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1107/S0907444908037591
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1107/S2052252518010552
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1002/pro.3353
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1093/bioinformatics/btr590
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1016/j.jmb.2016.02.002
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1107/S2059798316013036
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

http://dx.doi.org/10.1107/S2059798319003875
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:00.500504

A series of PDB related databases for everyday needs PubMed citations: 249.

249 articles citing: A series of PDB related databases for everyday needs

Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum. PMID:35865963
De novo design of discrete, stable 310-helix peptide assemblies. PMID:35732733
Characterization of mutations modulating enhanced transmissibility of SARS-CoV-2 B.1.617+ (Delta) variant using In Silico tools. PMID:35721780
The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. PMID:35622909
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. PMID:35438789
Cryo-EM structure of glycoprotein C from Crimean-Congo hemorrhagic fever virus. PMID:35234630
The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. PMID:35169801
Protein sequence design with a learned potential. PMID:35136054
Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. PMID:35030025
Helical structure motifs made searchable for functional peptide design. PMID:35013238
Biological factors in the synthetic construction of overlapping genes. PMID:34895142
Assessing the accuracy of contact and distance predictions in CASP14. PMID:34595772
Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures. PMID:34498035
Poor Person's pH Simulation of Membrane Proteins. PMID:34302678
Identification and Characterization of Specific Protein-Lipid Interactions Using Molecular Simulation. PMID:34302674
Deep Learning for Protein-Protein Interaction Site Prediction. PMID:34236667
Structural basis for the constitutive activity and immunomodulatory properties of the Epstein-Barr virus-encoded G protein-coupled receptor BILF1. PMID:34216564
Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? PMID:34200257
Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity. PMID:34197453
Engineering the protein dynamics of an ancestral luciferase. PMID:34127663
The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds. PMID:34015255
Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. PMID:33925854
Genome-editing approaches and applications: a brief review on CRISPR technology and its role in cancer. PMID:33732568
In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. PMID:33707507
Fisetin inhibits tau aggregation by interacting with the protein and preventing the formation of β-strands. PMID:33662414
SARS-CoV-2 spillover transmission due to recombination event. PMID:33615041
Are vanadium complexes druggable against the main protease Mpro of SARS-CoV-2? - A computational approach. PMID:33589845
Study on mechanism of matrine in treatment of COVID-19 combined with liver injury by network pharmacology and molecular docking technology. PMID:33517789
A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis. PMID:33454012
Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family. PMID:33433210
Evaluating Protein Transfer Learning with TAPE. PMID:33390682
PremPS: Predicting the impact of missense mutations on protein stability. PMID:33378330
Disclosing the Interaction of Gold Nanoparticles with Aβ(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations. PMID:33375086
Characterization of the Mycobacterial MSMEG-3762/63 Efflux Pump in Mycobacterium smegmatis Drug Efflux. PMID:33343518
Autochthonous Transmission of West Nile Virus by a New Vector in Iran, Vector-Host Interaction Modeling and Virulence Gene Determinants. PMID:33339336
Genetic interaction mapping informs integrative structure determination of protein complexes. PMID:33303586
MMP activation-associated aminopeptidase N reveals a bivalent 14-3-3 binding motif. PMID:33109610
Effects of Nucleotide and End-Dependent Actin Conformations on Polymerization. PMID:33080221
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. PMID:32857966
Structure of human Frizzled5 by fiducial-assisted cryo-EM supports a heterodimeric mechanism of canonical Wnt signaling. PMID:32762848
PremPRI: Predicting the Effects of Missense Mutations on Protein-RNA Interactions. PMID:32756481
Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aβ(1-40) Monomers by Means of Molecular Dynamics. PMID:32751722
Side chain flexibility and the symmetry of protein homodimers. PMID:32706779
Insight into vitronectin structural evolution on material surface chemistries: The mediation for cell adhesion. PMID:32695935
High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States. PMID:32683863
Structure-based designing efficient peptides based on p53 binding site residues to disrupt p53-MDM2/X interaction. PMID:32651397
On the complementarity of X-ray and NMR data. PMID:32647823
Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques. PMID:32587856
Coarse-grained (hybrid) integrative modeling of biomolecular interactions. PMID:32514329
High-Strength, Durable All-Silk Fibroin Hydrogels with Versatile Processability toward Multifunctional Applications. PMID:32440259
The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage. PMID:32260156
Sonification based de novo protein design using artificial intelligence, structure prediction, and analysis using molecular modeling. PMID:32206742
Mutation effect estimation on protein-protein interactions using deep contextualized representation learning. PMID:32166223
Effect of Phosphorylation and O-GlcNAcylation on Proline-Rich Domains of Tau. PMID:32065850
Structural and biophysical characterization of the type VII collagen vWFA2 subdomain leads to identification of two binding sites. PMID:32031736
Human αB-crystallin discriminates between aggregation-prone and function-preserving variants of a client protein. PMID:31812542
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins. PMID:31657215
Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations. PMID:31618974
Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility. PMID:31601934
SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. PMID:31570166
Biophysical Insight on the Membrane Insertion of an Arginine-Rich Cell-Penetrating Peptide. PMID:31505894
Modulation of Amyloid-β42 Conformation by Small Molecules Through Nonspecific Binding. PMID:31476124
Conformational Ensembles Exhibit Extensive Molecular Recognition Features. PMID:31459119
rawMSA: End-to-end Deep Learning using raw Multiple Sequence Alignments. PMID:31415569
Comparative structural and thermal stability studies of Cuc m 2.0101, Art v 4.0101 and other allergenic profilins. PMID:31326654
CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation. PMID:31317604
Prediction of interresidue contacts with DeepMetaPSICOV in CASP13. PMID:31298436
Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods. PMID:31245383
ProteinNet: a standardized data set for machine learning of protein structure. PMID:31185886
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. PMID:31161204
PrankWeb: a web server for ligand binding site prediction and visualization. PMID:31114880
Regulation of measles virus gene expression by P protein coiled-coil properties. PMID:31086822
Single nucleotide polymorphisms in the human ATP7B gene modify the properties of the ATP7B protein. PMID:31070637
Essential Mycoplasma Glycolipid Synthase Adheres to the Cell Membrane by Means of an Amphipathic Helix. PMID:31068620
Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance. PMID:31019050
Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features. PMID:30933973
The disordered plant dehydrin Lti30 protects the membrane during water-related stress by cross-linking lipids. PMID:30819802
Structural Analysis of a Trimer of β2-Microgloblin Fragment by Molecular Dynamics Simulations. PMID:30771855
Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. PMID:30737480
Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide. PMID:30692548
ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery. PMID:30601115
Helical Structure of Recombinant Melittin. PMID:30570258
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics. PMID:30568854
Fine mapping of hydrophobic contacts reassesses the organization of the first three dystrophin coiled-coil repeats. PMID:30468271
Prediction of Antimicrobial Potential of a Chemically Modified Peptide From Its Tertiary Structure. PMID:30416494
Automatically Fixing Errors in Glycoprotein Structures with Rosetta. PMID:30344107
Machine Learning Approaches for Protein⁻Protein Interaction Hot Spot Prediction: Progress and Comparative Assessment. PMID:30287797
Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces. PMID:30217822
DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. PMID:30209260
Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin. PMID:30188321
Structural Characterization of the Lactobacillus Plantarum FlmC Protein Involved in Biofilm Formation. PMID:30181476
Predicting the clinical impact of human mutation with deep neural networks. PMID:30038395
A coarse-grained approach to studying the interactions of the antimicrobial peptides aurein 1.2 and maculatin 1.1 with POPG/POPE lipid mixtures. PMID:30019106
Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation. PMID:29725062
The Preservation of Lyophilized Human Growth Hormone Activity: how Do Buffers and Sugars Interact? PMID:29700627
Supramolecular self assembly of nanodrill-like structures for intracellular delivery. PMID:29501722
Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. PMID:29401388
Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES. PMID:29279306
The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod. PMID:29129382
Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations. PMID:29053635
Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure. PMID:28991206
Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions. PMID:28966016
Host proteostasis modulates influenza evolution. PMID:28949290
Investigating Ebola virus pathogenicity using molecular dynamics. PMID:28812539
Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis Is Controlled by a Redox-Sensitive Thiol Switch. PMID:28786661
Structural insights into the function of ZRANB3 in replication stress response. PMID:28621305
Distribution of dipeptides in different protein structural classes: an effort to find new similarities. PMID:28612124
Albumin (BSA) adsorption onto graphite stepped surfaces. PMID:28595417
How do SMA-linked mutations of SMN1 lead to structural/functional deficiency of the SMA protein? PMID:28570645
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. PMID:28453681
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. PMID:28448138
Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure. PMID:28368281
Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice. PMID:28362841
An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements. PMID:28324365
Twilight reloaded: the peptide experience. PMID:28291756
Computational smart polymer design based on elastin protein mutability. PMID:28279921
Interaction of aurein 1.2 and its analogue with DPPC lipid bilayer. PMID:28130642
One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor. PMID:28076818
Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis. PMID:27803181
Death Receptor 5 Networks Require Membrane Cholesterol for Proper Structure and Function. PMID:27720987
GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features. PMID:27708373
Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD. PMID:27555327
The Ramachandran Number: An Order Parameter for Protein Geometry. PMID:27490241
ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins. PMID:27484738
Computational studies of human class V alcohol dehydrogenase - the odd sibling. PMID:27455956
Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. PMID:27437113
Molecular Dynamics Driven Design of pH-Stabilized Mutants of MNEI, a Sweet Protein. PMID:27340829
Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. PMID:27332813
MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. PMID:27150810
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. PMID:27138088
Automated structure modeling of large protein assemblies using crosslinks as distance restraints. PMID:27111507
Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations. PMID:27110669
Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective. PMID:27088597
Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium. PMID:27082435
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. PMID:27028541
Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses. PMID:27009368
Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. PMID:27003415
Unlocking the Bacterial SecY Translocon. PMID:26973090
Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. PMID:26829384
All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations. PMID:26817663
The effect of amidation on the behaviour of antimicrobial peptides. PMID:26745958
Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide. PMID:26602442
Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. PMID:26588568
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. PMID:26516349
An Exploration of the Universe of Polyglutamine Structures. PMID:26495838
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins. PMID:26439842
Structure and function of the Escherichia coli Tol-Pal stator protein TolR. PMID:26354441
Cardiolipin Interactions with Proteins. PMID:26300339
Membrane Interaction of the Glycosyltransferase WaaG. PMID:26244737
Secondary Structure of Rat and Human Amylin across Force Fields. PMID:26221949
Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens. PMID:26166706
Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae. PMID:26157620
Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis. PMID:26147762
Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2. PMID:26046940
CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events. PMID:25996941
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. PMID:25919886
Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1). PMID:25904995
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding. PMID:25808133
Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system. PMID:25800619
Phosphorylation of Atg31 is required for autophagy. PMID:25773276
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction. PMID:25750595
The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study. PMID:25750022
Structures of the Apo and FAD-bound forms of 2-hydroxybiphenyl 3-monooxygenase (HbpA) locate activity hotspots identified by using directed evolution. PMID:25737306
Structural and functional investigation of flavin binding center of the NqrC subunit of sodium-translocating NADH:quinone oxidoreductase from Vibrio harveyi. PMID:25734798
Protein models docking benchmark 2. PMID:25712716
Structural transitions and interactions in the early stages of human glucagon amyloid fibrillation. PMID:25692598
Comparison of three ionic liquid-tolerant cellulases by molecular dynamics. PMID:25692593
Structural and biochemical analysis of the essential diadenylate cyclase CdaA from Listeria monocytogenes. PMID:25605729
An approach to creating a more realistic working model from a protein data bank entry. PMID:25605595
Flies expand the repertoire of protein structures that bind ice. PMID:25561557
Fragment based group QSAR and molecular dynamics mechanistic studies on arylthioindole derivatives targeting the α-β interfacial site of human tubulin. PMID:25521775
The structural basis for receptor recognition of human interleukin-18. PMID:25500532
FadA5 a thiolase from Mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. PMID:25482540
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. PMID:25392418
Analysis of nidogen-1/laminin γ1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes. PMID:25387007
Exploring nicotinamide cofactor promiscuity in NAD(P)H-dependent flavin containing monooxygenases (FMOs) using natural variation within the phosphate binding loop. Structure and activity of FMOs from Cellvibrio sp. BR and Pseudomonas stutzeri NF13. PMID:25383040
Characteristics of protein residue-residue contacts and their application in contact prediction. PMID:25374390
Structural states of the flexible catalytic loop of M. tuberculosis tyrosyl-tRNA synthetase in different enzyme-substrate complexes. PMID:25373444
A series of PDB-related databanks for everyday needs. PMID:25352545
Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs. PMID:25307852
Investigation of the Josephin Domain protein-protein interaction by molecular dynamics. PMID:25268243
Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PMID:25222008
Structure and regulatory interactions of the cytoplasmic terminal domains of serotonin transporter. PMID:25093911
An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. PMID:25063439
In silico comparative characterization of pharmacogenomic missense variants. PMID:25057096
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. PMID:25006036
PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements. PMID:24995959
Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection. PMID:24926593
ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures. PMID:24923818
Factors that drive peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants. PMID:24915112
VarMod: modelling the functional effects of non-synonymous variants. PMID:24906884
Probing the average local structure of biomolecules using small-angle scattering and scaling laws. PMID:24896127
Prediction and redesign of protein-protein interactions. PMID:24878423
An experimentally determined evolutionary model dramatically improves phylogenetic fit. PMID:24859245
Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani. PMID:24849290
Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. PMID:24832673
Alpha-bulges in G protein-coupled receptors. PMID:24806342
PredictProtein--an open resource for online prediction of protein structural and functional features. PMID:24799431
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. PMID:24742328
The DynaMine webserver: predicting protein dynamics from sequence. PMID:24728994
Anomalies in the refinement of isoleucine. PMID:24699648
Molecular mechanism of Mg2+-dependent gating in CorA. PMID:24694723
A rapid, site-selective and efficient route to the dual modification of DARPins. PMID:24687090
A molecular interpretation of 2D IR protein folding experiments with Markov state models. PMID:24655511
Insight into conformational change for 14-3-3σ protein by molecular dynamics simulation. PMID:24552877
Folding of the RNA recognition motif (RRM) domains of the amyotrophic lateral sclerosis (ALS)-linked protein TDP-43 reveals an intermediate state. PMID:24497641
Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. PMID:24392845
Protein domains of unknown function are essential in bacteria. PMID:24381303
GPCRDB: an information system for G protein-coupled receptors. PMID:24304901
Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. PMID:24174543
Optimized atomic statistical potentials: assessment of protein interfaces and loops. PMID:24078704
Quality assessment of protein NMR structures. PMID:24060334
A conserved motif flags acyl carrier proteins for β-branching in polyketide synthesis. PMID:24056399
Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure. PMID:24044607
Exploiting tertiary structure through local folds for crystallographic phasing. PMID:24037245
Conformational stability of fibrillar amyloid-beta oligomers via protofilament pair formation - a systematic computational study. PMID:23936224
An overview of tools for the validation of protein NMR structures. PMID:23877928
Structural analysis of mitochondrial mutations reveals a role for bigenomic protein interactions in human disease. PMID:23874847
Conformational stability and activity analysis of two hydroxymethylbilane synthase mutants, K132N and V215E, with different phenotypic association with acute intermittent porphyria. PMID:23815679
Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. PMID:23811057
Structural and functional characterization of Pseudomonas aeruginosa AlgX: role of AlgX in alginate acetylation. PMID:23779107
nfxB as a novel target for analysis of mutation spectra in Pseudomonas aeruginosa. PMID:23762483
VLDP web server: a powerful geometric tool for analysing protein structures in their environment. PMID:23761450
Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes. PMID:23459159
New enumeration algorithm for protein structure comparison and classification. PMID:23445440
Designing and benchmarking the MULTICOM protein structure prediction system. PMID:23442819
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? PMID:23442792
The activity of prolactin releasing peptide correlates with its helicity. PMID:23426574
Mining tertiary structural motifs for assessment of designability. PMID:23422424
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure. PMID:23409953
Predicting functional effect of human missense mutations using PolyPhen-2. PMID:23315928
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. PMID:23262490
Modelling dynamics in protein crystal structures by ensemble refinement. PMID:23251785
Structure and dynamics of the second CARD of human RIG-I provide mechanistic insights into regulation of RIG-I activation. PMID:23063562
In silico modeling of the staphylococcal bacteriophage-derived peptidase CHAP(K). PMID:23050213
Structural differences between thermophilic and mesophilic membrane proteins. PMID:23001966
CING: an integrated residue-based structure validation program suite. PMID:22986687
Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases? PMID:22577357
Systematic analysis of metallo-β-lactamases using an automated database. PMID:22547615
Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen. PMID:22505400
Another case of fraud in structural biology. PMID:22505399
PDB_REDO: constructive validation, more than just looking for errors. PMID:22505269
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. PMID:22387432
ccPDB: compilation and creation of data sets from Protein Data Bank. PMID:22139939
Multi-scale genetic dynamic modelling I : an algorithm to compute generators. PMID:21487823
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655
PDB_REDO: automated re-refinement of X-ray structure models in the PDB PubMed citations: 106.

106 articles citing: PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. PMID:35887033
Serial macromolecular crystallography at ALBA Synchrotron Light Source. PMID:35511023
Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography. PMID:35507266
Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes. PMID:35141216
Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. PMID:35108401
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases. PMID:34998123
Discovery of a novel pseudo β-hairpin structure of N-truncated amyloid-β for use as a vaccine against Alzheimer's disease. PMID:34776512
Improving sampling of crystallographic disorder in ensemble refinement. PMID:34726164
Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control. PMID:34552077
A method for intuitively extracting macromolecular dynamics from structural disorder. PMID:34535675
New restraints and validation approaches for nucleic acid structures in PDB-REDO. PMID:34473084
Priming mycobacterial ESX-secreted protein B to form a channel-like structure. PMID:34337436
Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. PMID:34289059
Motions around conserved helical weak spots facilitate GPCR activation. PMID:34272892
Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses. PMID:34211469
Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice. PMID:33844653
Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii. PMID:33826169
Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective. PMID:33603257
Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis. PMID:33586945
An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase. PMID:33420418
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. PMID:33404525
The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms. PMID:33171880
A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI. PMID:33114370
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. PMID:32857966
Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase. PMID:32728686
Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. PMID:32681840
Structure, Dynamics and Cellular Insight Into Novel Substrates of the Legionella pneumophila Type II Secretion System. PMID:32656228
A Review of Deep Learning Methods for Antibodies. PMID:32354020
Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. PMID:31968260
Structure of Drosophila melanogaster ARC1 reveals a repurposed molecule with characteristics of retroviral Gag. PMID:31911950
Structural and Functional Analyses of Human ChaC2 in Glutathione Metabolism. PMID:31878259
Facilities that make the PDB data collection more powerful. PMID:31724231
A Consensus Binding Motif for the PP4 Protein Phosphatase. PMID:31585692
Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data. PMID:31373570
Sharp kinking of a coiled-coil in MutS allows DNA binding and release. PMID:31372631
Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system. PMID:31235958
Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans. PMID:31204053
Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. PMID:31076506
Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. PMID:30937380
An assessment of three human methylenetetrahydrofolate dehydrogenase/cyclohydrolase-ligand complexes following further refinement. PMID:30839287
Making glycoproteins a little bit sweeter with PDB-REDO. PMID:30084395
Automatic recognition of ligands in electron density by machine learning. PMID:30016407
Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements. PMID:29626214
Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role. PMID:29242189
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
The L33F darunavir resistance mutation acts as a molecular anchor reducing the flexibility of the HIV-1 protease 30s and 80s loops. PMID:29124158
A distance geometry-based description and validation of protein main-chain conformation. PMID:28989721
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. PMID:28977405
Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps. PMID:28815771
Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes. PMID:28591827
Structural Analysis of the Glucocorticoid Receptor Ligand-Binding Domain in Complex with Triamcinolone Acetonide and a Fragment of the Atypical Coregulator, Small Heterodimer Partner. PMID:28396564
Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. PMID:28233410
Crystal structure and structure-based mutagenesis of actin-specific ADP-ribosylating toxin CPILE-a as novel enterotoxin. PMID:28199340
A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1). PMID:27984042
A public database of macromolecular diffraction experiments. PMID:27841751
An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis. PMID:27810896
Validation and correction of Zn-CysxHisy complexes. PMID:27710932
Data publication with the structural biology data grid supports live analysis. PMID:26947396
Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis. PMID:26592762
Structural determinants of reductive terpene cyclization in iridoid biosynthesis. PMID:26551396
Structure of a fungal form of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans. PMID:26527262
Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. PMID:26287633
Detection of trans-cis flips and peptide-plane flips in protein structures. PMID:26249342
(Patho-)physiological relevance of PINK1-dependent ubiquitin phosphorylation. PMID:26162776
Building a virtual ligand screening pipeline using free software: a survey. PMID:26094053
Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli. PMID:25685666
An approach to creating a more realistic working model from a protein data bank entry. PMID:25605595
High accuracy of Karplus equations for relating three-bond J couplings to protein backbone torsion angles. PMID:25511552
Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PMID:25375667
Identification and structural analysis of an L-asparaginase enzyme from guinea pig with putative tumor cell killing properties. PMID:25320094
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
Operation of the Australian Store.Synchrotron for macromolecular crystallography. PMID:25286837
Structure of glutathione S-transferase 1 from the major human hookworm parasite Necator americanus (Na-GST-1) in complex with glutathione. PMID:25195885
The PDB_REDO server for macromolecular structure model optimization. PMID:25075342
Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. PMID:25075337
Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630. PMID:25004969
Refinement of macromolecular structures against neutron data with SHELXL2013. PMID:24587788
Improved crystallographic structures using extensive combinatorial refinement. PMID:24076406
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. PMID:23821665
Expectation bias and information content. PMID:23385742
Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. PMID:22868759
PDB_REDO: constructive validation, more than just looking for errors. PMID:22505269
Low-resolution refinement tools in REFMAC5. PMID:22505260
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. PMID:22505257
Towards automated crystallographic structure refinement with phenix.refine. PMID:22505256
Drug design for ever, from hype to hope. PMID:22252446
The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures. PMID:22246295
Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. PMID:22145047
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. PMID:22139937
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
X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery. PMID:21779303
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. PMID:21728306
Gaia: automated quality assessment of protein structure models. PMID:21700672
The role of Co²+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols. PMID:21505236
The evolving field of imaging mass spectrometry and its impact on future biological research. PMID:21322093
On the complexity of Engh and Huber refinement restraints: the angle τ as example. PMID:21123875
A series of PDB related databases for everyday needs. PMID:21071423
GPCRDB: information system for G protein-coupled receptors. PMID:21045054
Unmet challenges of structural genomics. PMID:20810277
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. PMID:20648263
Detection of unrealistic molecular environments in protein structures based on expected electron densities. PMID:20405167
Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. PMID:20152150
On the use of logarithmic scales for analysis of diffraction data. PMID:19966414
4D prediction of protein (1)H chemical shifts. PMID:19876601
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. PMID:19809795
http://dx.doi.org/10.1107/S0907444911054515
http://dx.doi.org/10.1107/S0021889809008784
http://dx.doi.org/10.1107/S0907444908037591

http://dx.doi.org/10.1107/S2052252518010552

http://dx.doi.org/10.1002/pro.3353

http://dx.doi.org/10.1093/bioinformatics/btr590

http://dx.doi.org/10.1016/j.jmb.2016.02.002

http://dx.doi.org/10.1107/S2059798316013036

http://dx.doi.org/10.1107/S2059798319003875

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protein
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protein structure
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x-ray diffraction
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structure analysis
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version: extracted_at: 2022-11-04T11:25:00.500504

protein protein structure x-ray diffraction structure analysis

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