Partner‐specific Prediction of RNA‐binding Residues in Proteins: A Critical Assessment

scientific article published on 30 December 2018

Partner‐specific Prediction of RNA‐binding Residues in Proteins: A Critical Assessment is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1002/PROT.25639
P932PMC publication ID6389706
P698PubMed publication ID30536635

P50authorVasant HonavarQ7916327
Drena DobbsQ54655970
Yong JungQ90400384
Yasser El-ManzalawyQ91396255
P2860cites workDiverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory systemQ21092736
Global changes in the RNA binding specificity of HIV-1 gag regulate virion genesisQ24498694
Comparative genomics and evolution of proteins involved in RNA metabolismQ24515041
The Protein Data BankQ24515306
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
SF1 and SF2 helicases: family mattersQ24596016
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolutionQ24630078
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIPQ24630900
Advances in the characterization of RNA-binding proteinsQ26738495
Computational Prediction of RNA-Binding Proteins and Binding SitesQ26779137
Computational prediction of protein interfaces: A review of data driven methodsQ26783912
Specificity and nonspecificity in RNA-protein interactionsQ26796990
High-throughput characterization of protein-RNA interactionsQ27013905
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence featuresQ27499023
A mechanistic overview of translation initiation in eukaryotesQ28268066
RNA-binding proteins in human genetic diseaseQ28285965
The nature of the accessible and buried surfaces in proteinsQ28296598
Computational modeling of protein-RNA complex structuresQ28299590
RNA-binding proteins: modular design for efficient functionQ28300258
RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteinsQ28538998
Progress and challenges in predicting protein interfacesQ28602320
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the artQ29026419
RNABindR: a server for analyzing and predicting RNA-binding sites in proteinsQ29031922
FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface ResiduesQ29306580
Regulation of mRNA translation and stability by microRNAsQ29547304
From birth to death: the complex lives of eukaryotic mRNAsQ29615021
RNA recognition motifs: boring? Not quiteQ29615153
RNA processing and its regulation: global insights into biological networksQ29615182
Assessing the accuracy of prediction algorithms for classification: an overviewQ29615358
The enzymes and control of eukaryotic mRNA turnoverQ29616563
Template-based modeling and free modeling by I-TASSER in CASP7.Q30364787
Impact of genetic variation on three dimensional structure and function of proteinsQ30491136
DISOPRED3: precise disordered region predictions with annotated protein-binding activityQ30633989
Partner-aware prediction of interacting residues in protein-protein complexes from sequence dataQ31043905
Specific RNA binding proteins constructed from zinc fingersQ32054225
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval.Q33551124
RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites.Q33677541
Non-Watson-Crick base pairs in RNA-protein recognitionQ33814857
HomPPI: a class of sequence homology based protein-protein interface prediction methodsQ33935448
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA dockingQ33996183
Prediction of dinucleotide-specific RNA-binding sites in proteinsQ34176444
ROCS: receiver operating characteristic surface for class-skewed high-throughput dataQ34336571
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.Q34865111
A multiple-template approach to protein threadingQ34975436
PAIRpred: partner-specific prediction of interacting residues from sequence and structureQ35045263
Salt contribution to RNA tertiary structure folding stabilityQ35079364
Sequence-specific binding of single-stranded RNA: is there a code for recognition?Q35128019
Antibody specific epitope prediction-emergence of a new paradigmQ35685171
SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding ResiduesQ35692167
Crystallization of RNA and RNA-protein complexesQ35869456
A Large-Scale Assessment of Nucleic Acids Binding Site Prediction ProgramsQ35872601
Structure determination of protein/RNA complexes by NMR.Q36088490
High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorderQ36160593
DSSR: an integrated software tool for dissecting the spatial structure of RNA.Q36337710
A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA SequenceQ36444304
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteinsQ37739405
Roles of intrinsic disorder in protein-nucleic acid interactionsQ37923321
Computational methods for prediction of protein-RNA interactionsQ37948500
Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing.Q37972715
RNA-binding proteins in Mendelian disease.Q38082164
Prediction of RNA binding proteins comes of age from low resolution to high resolutionQ38123046
Probing the structure of RNAs in solutionQ38181797
On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions.Q38195952
High throughput platform to explore RNA-protein interactomesQ38229626
Structural mechanisms of RNA recognition: sequence-specific and non-specific RNA-binding proteins and the Cas9-RNA-DNA complexQ38272498
A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues.Q38454986
Protein-RNA interactions: a structural analysisQ38658598
Protein-RNA interactions: structural biology and computational modeling techniquesQ38683195
Determinants of affinity and specificity in RNA-binding proteins.Q38868383
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks.Q39067587
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequencesQ39679865
A MOTIF-BASED METHOD FOR PREDICTING INTERFACIAL RESIDUES IN BOTH THE RNA AND PROTEIN COMPONENTS OF PROTEIN-RNA COMPLEXES.Q40098392
A novel approach to represent and compare RNA secondary structuresQ40164888
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteinsQ41010938
Computational learning on specificity-determining residue-nucleotide interactionsQ41834219
DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residuesQ42237296
Prediction of nucleic acid binding probability in proteins: a neighboring residue network based scoreQ42410843
Hidden specificity in an apparently nonspecific RNA-binding proteinQ42689235
The dataset for protein-RNA binding affinityQ42860933
Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteinsQ43284323
Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines.Q45966250
Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chainsQ47281430
Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structuresQ48431908
PRIdictor: Protein-RNA Interaction predictor.Q50765975
Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.Q50965878
Modeling of Protein-RNA Complex Structures Using Computational Docking Methods.Q51365159
PRINTR: prediction of RNA binding sites in proteins using SVM and profiles.Q51895497
A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins.Q51900421
A census of human RNA-binding proteinsQ58283908
Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)Q58642712
RNA-protein complexesQ71231806
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)198-211
P577publication date2018-12-30
P1433published inProteinsQ7251514
P1476titlePartner-specific prediction of RNA-binding residues in proteins: A critical assessment
P478volume87

Reverse relations

Q99604815Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Typecites workP2860

Search more.