IDP ontology
Ontology used to describe disordered regions in intrinsically disordered proteins.
Description
More detailed information about this field from each metasource.
Ontology used to describe disordered regions in intrinsically disordered proteins.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:59.960592
Webpage:
https://disprot.org/ontologyWebpage
More detailed information about this field from each metasource.
https://disprot.org/ontology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:59.960592
Licence:
Name: CC-BY-4.0Licence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
DisProt 7.0: a major update of the database of disordered proteins
PMID: 27899601
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:59.960592
DisProt: intrinsic protein disorder annotation in 2020
PMID: 31713636
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:59.960592
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
PMID: 34850135
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:59.960592
Publications
More detailed information about this field from each metasource.
DisProt 7.0: a major update of the database of disordered proteins
PMID: 27899601
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:59.960592
DisProt: intrinsic protein disorder annotation in 2020
PMID: 31713636
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:59.960592
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
PMID: 34850135
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:59.960592
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DisProt 7.0: a major update of the database of disordered proteins
PubMed citations: 83.
83 articles citing: DisProt 7.0: a major update of the database of disordered proteins
Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide. PMID:35835960
Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.). PMID:35454181
Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. PMID:35454150
MoRF-FUNCpred: Molecular Recognition Feature Function Prediction Based on Multi-Label Learning and Ensemble Learning. PMID:35350759
Identifying Intrinsically Disordered Protein Regions through a Deep Neural Network with Three Novel Sequence Features. PMID:35330096
Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Subsequence Propensities. PMID:35298807
A FRET-Based Biosensor for the Src N-Terminal Regulatory Element. PMID:35200356
Pan-cancer assessment of mutational landscape in intrinsically disordered hotspots reveals potential driver genes. PMID:35061901
The dynamic basis of structural order in proteins. PMID:34981860
Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. PMID:34710373
ProTG4: A Web Server to Approximate the Sequence of a Generic Protein From an in Silico Library of Translatable G-Quadruplex (TG4)-Mapped Peptides. PMID:34602814
p27Kip1, an Intrinsically Unstructured Protein with Scaffold Properties. PMID:34571903
Cryptic amyloidogenic regions in intrinsically disordered proteins: Function and disease association. PMID:34527192
On the roles of intrinsically disordered proteins and regions in cell communication and signaling. PMID:34461937
flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions. PMID:34290238
Updated SARS-CoV-2 single nucleotide variants and mortality association. PMID:34245452
FG nucleoporins feature unique patterns that distinguish them from other IDPs. PMID:34237287
Online biophysical predictions for SARS-CoV-2 proteins. PMID:33892639
Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation. PMID:33826337
Exploring the conformational dynamics and flexibility of intrinsically disordered HIV-1 Nef protein using molecular dynamic network approaches. PMID:33747706
Tuning intrinsic disorder predictors for virus proteins. PMID:33614158
Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins. PMID:33291838
Sequence Versus Composition: What Prescribes IDP Biophysical Properties? PMID:33267368
A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon's Information Theory. PMID:33267305
Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions. PMID:33260713
Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment. PMID:33191750
The Anti-Inflammatory Protein TNIP1 Is Intrinsically Disordered with Structural Flexibility Contributed by Its AHD1-UBAN Domain. PMID:33182596
Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. PMID:32973219
Protein Databases Related to Liquid-Liquid Phase Separation. PMID:32947964
Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins. PMID:32867340
IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions. PMID:32756939
Predicting Conformational Properties of Intrinsically Disordered Proteins from Sequence. PMID:32696367
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins. PMID:32525675
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. PMID:32379317
Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder. PMID:32349480
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. PMID:32173600
RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins. PMID:32112084
Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A. PMID:32088186
The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation. PMID:32034199
Dynamic conformational flexibility and molecular interactions of intrinsically disordered proteins. PMID:32020911
Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. PMID:31969649
InterPep2: global peptide-protein docking using interaction surface templates. PMID:31917413
Importance of Fluctuating Amino Acid Residues in Folding and Binding of Proteins. PMID:31908743
LLPSDB: a database of proteins undergoing liquid-liquid phase separation in vitro. PMID:31906602
The dark side of Alzheimer's disease: unstructured biology of proteins from the amyloid cascade signaling pathway. PMID:31894361
An intrinsically disordered proteins community for ELIXIR. PMID:31824649
Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins. PMID:31756104
Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins. PMID:31724233
ELM-the eukaryotic linear motif resource in 2020. PMID:31680160
Identification and Analysis of Long Repeats of Proteins at the Domain Level. PMID:31649924
DISOselect: Disorder predictor selection at the protein level. PMID:31642118
New insight into the mechanisms protecting bacteria during desiccation. PMID:31559453
Polymer effects modulate binding affinities in disordered proteins. PMID:31488718
An interplay of structure and intrinsic disorder in the functionality of peptidylarginine deiminases, a family of key autoimmunity-related enzymes. PMID:31342121
Disorder Atlas: Web-based software for the proteome-based interpretation of intrinsic disorder predictions. PMID:31326853
Systematic identification of recognition motifs for the hub protein LC8. PMID:31266884
Codon selection reduces GC content bias in nucleic acids encoding for intrinsically disordered proteins. PMID:31175370
The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins. PMID:31139867
INGA 2.0: improving protein function prediction for the dark proteome. PMID:31073595
Intrinsically Disordered Linkers Impart Processivity on Enzymes by Spatial Confinement of Binding Domains. PMID:31032817
Computational Prediction of MoRFs, Short Disorder-to-order Transitioning Protein Binding Regions. PMID:31007871
Quality and bias of protein disorder predictors. PMID:30914747
On the Need to Develop Guidelines for Characterizing and Reporting Intrinsic Disorder in Proteins. PMID:30793871
Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins. PMID:30445805
Decision-Tree Based Meta-Strategy Improved Accuracy of Disorder Prediction and Identified Novel Disordered Residues Inside Binding Motifs. PMID:30301243
Zn2+-binding in the glutamate-rich region of the intrinsically disordered protein prothymosin-alpha. PMID:30187212
IDP⁻CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields. PMID:30135358
Protein Sequences Recapitulate Genetic Code Evolution. PMID:30002789
IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. PMID:30002402
Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model. PMID:29925017
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. PMID:29860432
Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii. PMID:29717210
Pi-Pi contacts are an overlooked protein feature relevant to phase separation. PMID:29424691
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
Platelet phosphorylated TDP-43: an exploratory study for a peripheral surrogate biomarker development for Alzheimer's disease. PMID:29134122
Random protein sequences can form defined secondary structures and are well-tolerated in vivo. PMID:29133927
The PROSECCO server for chemical shift predictions in ordered and disordered proteins. PMID:29119515
Prediction of protein disorder based on IUPred. PMID:29076577
MFIB: a repository of protein complexes with mutual folding induced by binding. PMID:29036655
Hotspots of age-related protein degradation: the importance of neighboring residues for the formation of non-disulfide crosslinks derived from cysteine. PMID:28592682
How disordered is my protein and what is its disorder for? A guide through the "dark side" of the protein universe. PMID:28232901
Time, space, and disorder in the expanding proteome universe. PMID:28145059 -
DisProt: intrinsic protein disorder annotation in 2020
PubMed citations: 78.
78 articles citing: DisProt: intrinsic protein disorder annotation in 2020
Compositional Bias of Intrinsically Disordered Proteins and Regions and Their Predictions. PMID:35883444
IDPsBind: a repository of binding sites for intrinsically disordered proteins complexes with known 3D structures. PMID:35883018
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning. PMID:35767567
Complementarity of the residue-level protein function and structure predictions in human proteins. PMID:35615015
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. PMID:35610022
AlphaFold2: A Role for Disordered Protein/Region Prediction? PMID:35562983
Predicting Protein Conformational Disorder and Disordered Binding Sites. PMID:35507260
Deep learning in prediction of intrinsic disorder in proteins. PMID:35356546
MoRF-FUNCpred: Molecular Recognition Feature Function Prediction Based on Multi-Label Learning and Ensemble Learning. PMID:35350759
Secretory quality control constrains functional selection-associated protein structure innovation. PMID:35338247
Identifying Intrinsically Disordered Protein Regions through a Deep Neural Network with Three Novel Sequence Features. PMID:35330096
Characterization of intrinsically disordered regions in proteins informed by human genetic diversity. PMID:35275927
Databases for intrinsically disordered proteins. PMID:35102880
Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins. PMID:35054576
Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates. PMID:35053240
A Thermodynamic Atlas of Proteomes Reveals Energetic Innovation across the Tree of Life. PMID:35038744
Current status of PTMs structural databases: applications, limitations and prospects. PMID:35020020
ECO: the Evidence and Conclusion Ontology, an update for 2022. PMID:34986598
The dynamic basis of structural order in proteins. PMID:34981860
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. PMID:34850135
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution. PMID:34810219
Identification of ligand binding sites in intrinsically disordered proteins with a differential binding score. PMID:34799573
FuzDB: a new phase in understanding fuzzy interactions. PMID:34791357
DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence. PMID:34765094
The Eukaryotic Linear Motif resource: 2022 release. PMID:34718738
Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. PMID:34710373
Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions. PMID:34680048
In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model. PMID:34638925
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. PMID:34606614
Selective 1 Hα NMR Methods Reveal Functionally Relevant Proline cis/trans Isomers in Intrinsically Disordered Proteins: Characterization of Minor Forms, Effects of Phosphorylation, and Occurrence in Proteome. PMID:34585830
Cryptic amyloidogenic regions in intrinsically disordered proteins: Function and disease association. PMID:34527192
Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure. PMID:34480923
On the roles of intrinsically disordered proteins and regions in cell communication and signaling. PMID:34461937
Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder. PMID:34360678
flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions. PMID:34290238
Evolutionary conservation of intrinsically unstructured regions in slit-diaphragm proteins. PMID:34288970
The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. PMID:34285781
Updated SARS-CoV-2 single nucleotide variants and mortality association. PMID:34245452
FG nucleoporins feature unique patterns that distinguish them from other IDPs. PMID:34237287
Pretraining model for biological sequence data. PMID:34050350
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation. PMID:34048569
QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores. PMID:34025946
Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids. PMID:33976321
SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes. PMID:33974039
Variants in GCNA, X-linked germ-cell genome integrity gene, identified in men with primary spermatogenic failure. PMID:33963445
Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars. PMID:33926372
APICURON: a database to credit and acknowledge the work of biocurators. PMID:33882120
A community effort to bring structure to disorder. PMID:33875888
Critical assessment of protein intrinsic disorder prediction. PMID:33875885
Tuning intrinsic disorder predictors for virus proteins. PMID:33614158
Computational Screening of Phase-separating Proteins. PMID:33610793
The human O-GlcNAcome database and meta-analysis. PMID:33479245
The complexity of protein interactions unravelled from structural disorder. PMID:33417598
Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. PMID:33398234
APOD: accurate sequence-based predictor of disordered flexible linkers. PMID:33381830
Assessing the low complexity of protein sequences via the low complexity triangle. PMID:33378336
The Role of Protein Disorder in Nuclear Transport and in Its Subversion by Viruses. PMID:33321790
Widespread occurrence of the droplet state of proteins in the human proteome. PMID:33318217
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. PMID:33305318
NeProc predicts binding segments in intrinsically disordered regions without learning binding region sequences. PMID:33304713
Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins. PMID:33291838
Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions. PMID:33260713
MobiDB: intrinsically disordered proteins in 2021. PMID:33237329
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. PMID:33119751
DescribePROT: database of amino acid-level protein structure and function predictions. PMID:33119734
Susceptibility of Protein Methionine Oxidation in Response to Hydrogen Peroxide Treatment-Ex Vivo Versus In Vitro: A Computational Insight. PMID:33066324
A Novel Strategy for the Development of Vaccines for SARS-CoV-2 (COVID-19) and Other Viruses Using AI and Viral Shell Disorder. PMID:33006287
IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell. PMID:32997198
Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. PMID:32973219
Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins. PMID:32867340
Variable absorption of mutational trends by prion-forming domains during Saccharomycetes evolution. PMID:32844065
DispHred: A Server to Predict pH-Dependent Order-Disorder Transitions in Intrinsically Disordered Proteins. PMID:32823616
Moonlighting Proteins in the Fuzzy Logic of Cellular Metabolism. PMID:32751110
Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. PMID:32599863
The Future of Protein Secondary Structure Prediction Was Invented by Oleg Ptitsyn. PMID:32560074
Genomic Analysis of Intrinsically Disordered Proteins in the Genus Camelus. PMID:32503351
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. PMID:32421769
Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins. PMID:32294448 -
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
PubMed citations: 2.
2 articles citing: DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro. PMID:35025997
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:34986604
Tags:
Tags
More detailed information about this field from each metasource.
protein disordered structure
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:59.960592
Tags
More detailed information about this field from each metasource.
protein disordered structure
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:59.960592
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