The unfoldomics decade: an update on intrinsically disordered proteins.

scientific article

The unfoldomics decade: an update on intrinsically disordered proteins. is …
instance of (P31):
scholarly articleQ13442814

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P6179Dimensions Publication ID1041073895
P356DOI10.1186/1471-2164-9-S2-S1
P932PMC publication ID2559873
P698PubMed publication ID18831774

P50authorVladimir VacicQ42850794
Vladimir N. UverskyQ59698496
P2093author name stringPedro Romero
A Keith Dunker
Jingwei Meng
Christopher J Oldfield
Zoran Obradovic
Jack Y Yang
Jessica Walton Chen
P2860cites workCalmodulin signaling: analysis and prediction of a disorder-dependent molecular recognitionQ82627891
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Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complexQ24336704
Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architectureQ24535935
Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organismsQ24548466
Nucleation, rapid folding, and globular intrachain regions in proteinsQ24564344
Altered phosphorylation and intracellular distribution of a (CUG)n triplet repeat RNA-binding protein in patients with myotonic dystrophy and in myotonin protein kinase knockout miceQ24654728
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A database of protein structure families with common folding motifsQ24676220
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Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and 3'-phosphoadenosine 5'-phosphate. Rationale for specificity differences between prototypical SULT2A1 and the SULT2BG1 isoformsQ27641844
Alternative splicing of Rac1 generates Rac1b, a self-activating GTPaseQ27642578
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Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structuresQ27731497
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Mechanisms of alternative pre-messenger RNA splicingQ28131822
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Intrinsically disordered proteinQ28191444
Domain combinations in archaeal, eubacterial and eukaryotic proteomesQ28203959
How did alternative splicing evolve?Q35930718
Aberrant and alternative splicing in cancerQ35936123
Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theoriesQ35963371
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signalingQ36226283
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discoveryQ36294114
Targeting protein-protein interactions for cancer therapyQ36311496
Automated protein function prediction--the genomic challengeQ36505962
Structural characterization of proteins using residue environmentsQ36789994
Looking into live cells with in-cell NMR spectroscopyQ36821672
NACP, a protein implicated in Alzheimer's disease and learning, is natively unfoldedQ36830682
Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorderQ36869604
Characterization of molecular recognition features, MoRFs, and their binding partnersQ36944291
Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regionsQ36986347
TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorderQ37178764
Amyloidogenesis of natively unfolded proteinsQ37184755
Structural Aspects of the Fibrinogen to Fibrin ConversionQ39935581
Mechanism of coupled folding and binding of an intrinsically disordered proteinQ40210194
Small-molecule antagonists of p53-MDM2 binding: research tools and potential therapeutics.Q40581450
Close encounters: why unstructured, polymeric domains can increase rates of specific macromolecular associationQ40823855
Design of a synthetic Mdm2-binding mini protein that activates the p53 response in vivo.Q41063629
Translational control of p27Kip1 accumulation during the cell cycleQ41213467
Alzheimer's disease-like phosphorylation of the microtubule-associated protein tau by glycogen synthase kinase-3 in transfected mammalian cells.Q41423732
Inhibitors of the Cip/Kip family.Q41710956
Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regionsQ41851853
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descentQ42415695
Intrinsic disorder in cell-signaling and cancer-associated proteinsQ28207698
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarraysQ28235146
Analysis of molecular recognition features (MoRFs)Q28260253
Redesigning enzyme topology by directed evolutionQ28265020
One thousand families for the molecular biologistQ28266140
The anatomy and taxonomy of protein structureQ28277011
Distinct and opposite activities of human terminal deoxynucleotidyltransferase splice variantsQ28281082
Shuffled domains in extracellular proteinsQ28288029
Solvent-induced collapse of alpha-synuclein and acid-denatured cytochrome cQ28361893
Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversityQ28910326
p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein foldingQ28910366
Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structureQ28910456
The molecular surface packageQ29039306
A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic DataQ29395063
Reaching for high-hanging fruit in drug discovery at protein-protein interfacesQ29547258
Lethality and centrality in protein networksQ29547267
Principles of CDK regulationQ29547820
Evidence for dynamically organized modularity in the yeast protein-protein interaction networkQ29614449
Why are "natively unfolded" proteins unstructured under physiologic conditions?Q29615739
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigmQ29615865
An evolutionary trace method defines binding surfaces common to protein familiesQ29615880
SCOP database in 2004: refinements integrate structure and sequence family dataQ29615988
Intrinsic disorder and protein functionQ29616415
Natively unfolded proteins: a point where biology waits for physicsQ29616416
Coupling of folding and binding for unstructured proteinsQ29616417
Coupling of local folding to site-specific binding of proteins to DNAQ29616464
Role of the ubiquitin-proteasome pathway in regulating abundance of the cyclin-dependent kinase inhibitor p27Q29617346
Small-molecule inhibitors of protein-protein interactions: progressing towards the dreamQ29617758
Why genes in pieces?Q29618207
Alternative splicing: increasing diversity in the proteomic worldQ29618730
Local structural disorder imparts plasticity on linear motifs.Q30158016
Protein structure and enzyme action.Q30334053
Comparing and combining predictors of mostly disordered proteins.Q30350136
Flexible nets. The roles of intrinsic disorder in protein interaction networks.Q30351593
Length-dependent prediction of protein intrinsic disorder.Q30353929
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.Q30360720
Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.Q30360723
Assessment of disorder predictions in CASP7.Q30363273
Characterizing the microenvironment surrounding protein sitesQ30417434
Structural basis for the attachment of a paramyxoviral polymerase to its templateQ30448746
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?Q42625650
Evaluation of features for catalytic residue prediction in novel foldsQ42958224
Protein dynamics in living cellsQ43153025
Splice variants: a homology modeling approachQ44745632
The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinsically disordered proteins that fold upon binding to their physiological partnerQ44746385
Alternative splicing in the N-terminus of Alzheimer's presenilin 1.Q45104033
Rational drug design via intrinsically disordered proteinQ47193604
Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomersQ47609385
Preformed structural elements feature in partner recognition by intrinsically unstructured proteinsQ47692263
Flavors of protein disorderQ47700031
Protein disorder and the evolution of molecular recognition: theory, predictions and observationsQ47715145
Coupled folding and binding with alpha-helix-forming molecular recognition elementsQ48122045
Combining prediction, computation and experiment for the characterization of protein disorder.Q51635477
Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs.Q51936092
Assessment of disorder predictions in CASP6.Q51963679
The protein trinity--linking function and disorder.Q52055900
Intrinsic disorder is a key characteristic in partners that bind 14-3-3 proteins.Q52664522
Disorder and sequence repeats in hub proteins and their implications for network evolution.Q52673882
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.Q52971558
Signal transduction via unstructured protein conduits.Q53491312
Macromolecular crowding in the Escherichia coli periplasm maintains alpha-synuclein disorder.Q54473816
Evaluation of disorder predictions in CASP5Q57972076
Probabilistic model of the human protein-protein interaction networkQ58482561
Unspinning the webQ59087483
Adenovirus amazes at Cold Spring HarborQ64382281
Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetaseQ70398900
Predicting Disordered Regions from Amino Acid Sequence: Common Themes Despite Differing Structural CharacterizationQ73174424
Predicting Binding Regions within Disordered ProteinsQ73174434
Light-scattering study of effect of electrolytes on alpha- and beta-casein solutionsQ73556264
The protein non-folding problem: amino acid determinants of intrinsic order and disorderQ73658941
Intrinsic protein disorder in complete genomesQ77145749
Effects of macromolecular crowding on the intrinsically disordered proteins c-Fos and p27(Kip1)Q77366460
Abundance of intrinsic disorder in protein associated with cardiovascular diseaseQ80181937
Intrinsic disorder in yeast transcriptional regulatory networkQ80353265
Virtual identification of essential proteins within the protein interaction network of yeastQ81466184
Optimizing long intrinsic disorder predictors with protein evolutionary informationQ81484824
Antagonists of protein-protein interactions.Q30861865
The N-terminal domain of p53 is natively unfolded.Q30879982
Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutionsQ31072074
Intrinsic disorder in the Protein Data BankQ31090109
Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleasesQ32032853
Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E.Q33204492
Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomesQ33252616
Composition Profiler: a tool for discovery and visualization of amino acid composition differencesQ33288198
Inferring function using patterns of native disorder in proteinsQ33295214
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partnersQ33325589
InterPro: an integrated documentation resource for protein families, domains and functional sitesQ33961349
Normalization of nomenclature for peptide motifs as ligands of modular protein domainsQ34120337
FlgM gains structure in living cellsQ34189211
Structural genomics analysis of alternative splicing and application to isoform structure modelingQ34244987
DisProt: a database of protein disorderQ34341031
Protein-protein interactions and cancer: small molecules going in for the killQ34424260
Gene family evolution and homology: genomics meets phylogeneticsQ34433357
Analysis of protein-protein interaction sites using surface patchesQ34439363
What does it mean to be natively unfolded?Q34488954
Function of alternative splicingQ34554255
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolutionQ34585750
Neuropathology, biochemistry, and biophysics of alpha-synuclein aggregationQ34648491
Mining alpha-helix-forming molecular recognition features with cross species sequence alignmentsQ34708119
Fuzzy complexes: polymorphism and structural disorder in protein-protein interactionsQ34720702
Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27 Kip1.Q34733508
Identification and functions of usefully disordered proteinsQ34989882
Speeding molecular recognition by using the folding funnel: the fly-casting mechanismQ35189399
A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disordersQ35212177
Protein folding revisited. A polypeptide chain at the folding ? misfolding ? nonfolding cross-roads: which way to go?Q35549177
Intrinsic disorder and functional proteomicsQ35632957
Inhibition of the p53-MDM2 interaction: targeting a protein-protein interface.Q35646494
Splice variants of G protein-coupled receptorsQ35679333
firestar--prediction of functionally important residues using structural templates and alignment reliabilityQ35914235
P407language of work or nameEnglishQ1860
P304page(s)S1
P577publication date2008-09-16
P1433published inBMC GenomicsQ15765854
P1476titleThe unfoldomics decade: an update on intrinsically disordered proteins.
P478volume9 Suppl 2

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Q38257180Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins
Q39183554Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins
Q41809289Proteomic phenotyping of Novosphingobium nitrogenifigens reveals a robust capacity for simultaneous nitrogen fixation, polyhydroxyalkanoate production, and resistance to reactive oxygen species
Q51112497Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau.
Q38589800Recombinant Intrinsically Disordered Proteins for NMR: Tips and Tricks
Q33766662Refining orthologue groups at the transcript level
Q37255426Residual structure within the disordered C-terminal segment of p21(Waf1/Cip1/Sdi1) and its implications for molecular recognition.
Q30379606SDSL-ESR-based protein structure characterization.
Q33978783SPA: Short peptide analyzer of intrinsic disorder status of short peptides
Q37440289Sending signals dynamically
Q33997189Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population.
Q42124997Small acid-soluble proteins with intrinsic disorder are required for UV resistance in Myxococcus xanthus spores
Q42151102Specificity and affinity quantification of flexible recognition from underlying energy landscape topography
Q51362509Stochastic simulation of structural properties of natively unfolded and denatured proteins.
Q33640276Structural disorder within Henipavirus nucleoprotein and phosphoprotein: from predictions to experimental assessment
Q34680376Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins
Q42707053Structural flexibility allows the functional diversity of potyvirus genome-linked protein VPg
Q27658157Structure of the Flexible Amino-Terminal Domain of Prion Protein Bound to a Sulfated Glycan
Q36638977Structure-based Inhibitor Design for the Intrinsically Disordered Protein c-Myc
Q36020398Targeting intrinsically disordered proteins in neurodegenerative and protein dysfunction diseases: another illustration of the D(2) concept
Q57043848The 124202 candidate effector ofMelampsora larici-populinainteracts with membranes inNicotianaandArabidopsis
Q40326289The BECN1 N-terminal domain is intrinsically disordered
Q30009088The Disordered Region of the HCV Protein NS5A: Conformational Dynamics, SH3 Binding, and Phosphorylation
Q39957451The challenge of increasing Pfam coverage of the human proteome
Q28080017The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease
Q34264016The dynamics of signal amplification by macromolecular assemblies for the control of chromosome segregation
Q30361131The evolution of protein structures and structural ensembles under functional constraint.
Q51066033The functional roles of the unstructured N- and C-terminal regions in αB-crystallin and other mammalian small heat-shock proteins.
Q27685219The hepatitis B virus preS1 domain hijacks host trafficking proteins by motif mimicry
Q34251310The hepatitis E virus polyproline region is involved in viral adaptation
Q33977801The high-molecular-weight kininogen domain 5 is an intrinsically unstructured protein and its interaction with ferritin is metal mediated.
Q42252683The human selenoprotein VCP-interacting membrane protein (VIMP) is non-globular and harbors a reductase function in an intrinsically disordered region
Q39850928The interaction between the measles virus nucleoprotein and the Interferon Regulator Factor 3 relies on a specific cellular environment
Q28749496The intrinsically disordered N-terminal domain of thymidylate synthase targets the enzyme to the ubiquitin-independent proteasomal degradation pathway
Q39032659The multifaceted benefits of protein co-expression in Escherichia coli
Q38527462The multifaceted roles of intrinsic disorder in protein complexes
Q37462521The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome
Q34046537The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation.
Q35907671The relationship between proteome size, structural disorder and organism complexity
Q37938718The role of protein disorder in the 14-3-3 interaction network
Q38806231Therapeutic Interventions of Cancers Using Intrinsically Disordered Proteins as Drug Targets: c-Myc as Model System.
Q41650438Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS.
Q53143914Troponins, intrinsic disorder, and cardiomyopathy.
Q51060526Tuning the precision of predictors to reduce overestimation of protein disorder over large datasets.
Q30385084Understanding protein non-folding.
Q36821293Understanding the structural ensembles of a highly extended disordered protein
Q27660091Urea denatured state ensembles contain extensive secondary structure that is increased in hydrophobic proteins
Q27012942What macromolecular crowding can do to a protein
Q46237020Zoonotic Hepatitis E Virus: An Ignored Risk for Public Health

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