Structure and function based selection of best predictors for identifying the binding sites in RNA binding proteins

Data sets

FamilyDataset( PDB-ids with chain details )
Anticodon-binding domain1ASY:A,1C0A:A
Anticodon-binding domain of Class II aaRS1H4S:A,1QF6:A
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases1F7U:A,1U0B:B
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases1FFY:A
Archaeal tRNA CCA-adding enzyme1TFW:A
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain1F7U:A
C-terminal domain of ProRS1H4S:A
C-terminal domain of glutamyl-tRNA synthetase (GluRS)1N78:A
C-terminal domain of ribosomal protein L21VQO:A
C-terminal fragment of elongation factor SelB1WSU:A
Canonical RBD1A9N:B,1FXL:A,2VOO:A
Class I aminoacyl-tRNA synthetases (RS), catalytic domain1F7U:A,1FFY:A,1J1U:A,1N78:A,1QTQ:A,1U0B:B,2AZX:A
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain1ASY:A,1C0A:A,1H4S:A,1QF6:A,1SER:A
Cold shock DNA-binding domain-like1VQO:A,2A8V:A,2ASB:A,2VNU:D,2VQE:Q
Comoviridae-like VP1PGL:2
Double-stranded RNA-binding domain (dsRBD)2NUG:A
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain1B23:P
EV matrix protein1H2C:A
Elongation factors1B23:P
Eukaryotic type KH-domain (KH-domain type I)1EC6:A
Fungal ribonucleases1B2M:A
G proteins1B23:P
GAD domain1C0A:A
Hut operon positive regulatory protein HutP1WPU:A
L30e/L7ae ribosomal proteins1SDS:A
La domain2VOO:A
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain1OOA:A
NSP3 homodimer1KNZ:A
Nop domain2OZB:B
PAZ domain1SI3:A
PIWI domain2BGG:A
PUA domain1K8W:A
Pleiotropic translational regulator Hfq1KQ2:A
Poly A polymerase head domain-like1VFG:A
Poly(A) polymerase, PAP2Q66:A
Post formyltransferase domain2FMT:A
Prokaryotic ribosomal protein L172J01:R
Prokaryotic type KH domain \(KH-domain type II\)2ASB:A,2UUB:C
Pseudouridine synthase II TruB1K8W:A
Pumilio repeat1M8X:A
RNA bacteriophage capsid protein2BU1:A
RNA-dependent RNA-polymerase1N35:A,1NB7:A,1UVJ:A,2E9T:A
RNB domain-like2VNU:D
RNase III catalytic domain-like2NUG:A
RNase Z-like2FK6:A
Rel/Dorsal transcription factors, DNA-binding domain1OOA:A
Rhabdovirus nucleocapsid protein2GIC:A
Rho termination factor, N-terminal domain2A8V:A
Ribonuclease PH domain2JEA:A,2JEA:B
Ribosomal protein L12HW8:A
Ribosomal protein L101VQO:G
Ribosomal protein L10e1VQO:H
Ribosomal protein L11, C-terminal domain1VQO:I
Ribosomal protein L131VQO:J
Ribosomal protein L141VQO:K
Ribosomal protein L18 and S111VQO:N,2VQE:K
Ribosomal protein L192J01:T
Ribosomal protein L19 (L19e)1VQO:P
Ribosomal protein L202J01:U
Ribosomal protein L21p2J01:V
Ribosomal protein L221VQO:R,2J01:W
Ribosomal protein L24e1VQO:U
Ribosomal protein L25-like1DFU:P,1FEU:A
Ribosomal protein L282J01:1
Ribosomal protein L29 (L29p)1VQO:V,2J01:2
Ribosomal protein L31VQO:B,2J01:E
Ribosomal protein L30p/L7e1VQO:W,2J01:3
Ribosomal protein L31e1VQO:X
Ribosomal protein L31p2J01:4
Ribosomal protein L32e1VQO:Y
Ribosomal protein L32p2J01:5
Ribosomal protein L35p2J01:8
Ribosomal protein L37ae1VQO:Z
Ribosomal protein L41VQO:C
Ribosomal protein L44e1VQO:3
Ribosomal protein L51VQO:D
Ribosomal protein L61VQO:E,2J01:H
Ribosomal protein L92J01:I
Ribosomal protein S102VQE:J
Ribosomal protein S132VQE:M
Ribosomal protein S142VQE:N
Ribosomal protein S182VQE:R
Ribosomal protein S22VQE:B
Ribosomal protein S202VQE:T
Ribosomal protein S3 C-terminal domain2UUB:C
Ribosomal protein S42VQE:D
Ribosomal protein S62VQE:F
Ribosomal protein S72VQE:G
Ribosomal protein S82VQE:H
Ribosomal proteins L15p and L18e1VQO:L,2J01:P
Ribosomal proteins L24p and L21e1VQO:T,1VQO:Q
Ribosome complexes2VQE:L,2VQE:O,2VQE:P,2VQE:S
RoRNP C-terminal domain-like1YVP:A
Seryl-tRNA synthetase (SerRS)1SER:A
Signal peptide-binding domain1HQ1:A
Sm motif of small nuclear ribonucleoproteins, SNRNP1M8V:A
Small subunit2VQE:E
TGS domain1QF6:A
TRAM domain2BH2:A
TROVE domain-like1YVP:A
Tandem AAA-ATPase domain2J0S:A
Threonyl-tRNA synthetase (ThrRS), second 'additional' domain1QF6:A
Tombusvirus P19 core protein, VP191R9F:A
Translational machinery components2VQE:I
Tymoviridae-like VP1DDL:A
ValRS/IleRS/LeuRS editing domain1FFY:A
Z-DNA binding domain2GXB:A
dsRNA phage RNA-dependent RNA-polymerase1UVJ:A
mRNA cap methylase1AV6:A
tRNA-guanine transglycosylase1Q2R:A
tRNA-intron endonuclease catalytic domain-like2GJW:A

Reference:  Prediction of RNA binding residues: An extensive analysis based on structure and function to select the best predictor
                    Nagarajan, R. and Gromiha, M. M.
                    PLoS One (2014), 9 (3), e91140.

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