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




Data sets

SuperfamilyDataset( PDB-ids with chain details )
"Winged helix" binding domain1WSU:A,2GXB:A,2VOO:A
ARM repeat1M8X:A
Alpha-L RNA-binding motif2VQE:D
An anticodon-binding domain of class I aminoacyl-tRNA synthetases1N78:A
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases1FFY:A,1U0B:B
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain1F7U:A
C-terminal domain of ProRS1H4S:A
Class II aaRS ABD-related1QF6:A
Class II aaRS and biotin synthetases1ASY:A,1C0A:A,1H4S:A,1QF6:A,1SER:A
DNA/RNA polymerases1N35:A,1NB7:A,1UVJ:A,2E9T:A
E set domains1OOA:A
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain1B23:P
EV matrix protein1H2C:A
Eukaryotic type KH-domain (KH-domain type I)1EC6:A
Formyltransferase2FMT:A
GAD domain-like1C0A:A
Glucocorticoid receptor-like (DNA-binding domain)1VQO:U,2VQE:N
Hut operon positive regulatory protein HutP1WPU:A
L domain-like1A9N:A
L21p-like2J01:V
L28p-like2J01:1,2J01:4
L30e-like1SDS:A
L35p-like2J01:8
L9 N-domain-like2J01:I
Metallo-hydrolase/oxidoreductase2FK6:A
Microbial ribonucleases1B2M:A,1JBS:A
NSP3 homodimer1KNZ:A
Nop domain2OZB:B
Nucleic acid-binding proteins1ASY:A,1C0A:A,1VQO:A,2A8V:A,2ASB:A,2BH2:A,2VNU:D,2VQE:Q
Nucleotidyltransferase1TFW:A,1VFG:A,2Q66:A
Nucleotidylyl transferase1F7U:A,1FFY:A,1J1U:A,1N78:A,1QTQ:A,1U0B:B,2AZX:A
P-loop containing nucleoside triphosphate hydrolases1B23:P,2J0S:A
PAP/OAS1 substrate-binding domain1TFW:A,2Q66:A
PAZ domain1SI3:A
PUA domain-like1K8W:A
Poly A polymerase C-terminal region-like1VFG:A
Positive stranded ssRNA viruses1DDL:A,1PGL:2
Prokaryotic ribosomal protein L172J01:R
Prokaryotic type KH domain (KH-domain type II)2ASB:A,2UUB:C
Pseudouridine synthase1K8W:A
RL5-like1VQO:D
RNA bacteriophage capsid protein2BU1:A
RNA-binding domain, RBD1A9N:B,1FXL:A,2VOO:A
RNase III domain-like2NUG:A
Rhabdovirus nucleoprotein-like2GIC:A
Rho N-terminal domain-like2A8V:A
Ribonuclease H-like2BGG:A
Ribonuclease PH domain 2-like2JEA:B,2JEA:A
Ribosomal protein L12HW8:A
Ribosomal protein L101VQO:G
Ribosomal protein L11, C-terminal domain1VQO:I
Ribosomal protein L131VQO:J
Ribosomal protein L141VQO:K
Ribosomal protein L16p/L10e1VQO:H
Ribosomal protein L19 (L19e)1VQO:P
Ribosomal protein L202J01:U
Ribosomal protein L221VQO:R,2J01:W
Ribosomal protein L25-like1DFU:P,1FEU:A,1QTQ:A
Ribosomal protein L29 (L29p)1VQO:V,2J01:2
Ribosomal protein L30p/L7e1VQO:W,2J01:3
Ribosomal protein L31e1VQO:X
Ribosomal protein L32e1VQO:Y
Ribosomal protein L41VQO:C
Ribosomal protein L61VQO:E,2J01:H
Ribosomal protein L9 C-domain2J01:I
Ribosomal protein S102VQE:J
Ribosomal protein S182VQE:R
Ribosomal protein S22VQE:B
Ribosomal protein S202VQE:T
Ribosomal protein S3 C-terminal domain2UUB:C
Ribosomal protein S5 domain 2-like2JEA:A,2JEA:B,2VQE:I
Ribosomal protein S62VQE:F
Ribosomal protein S72VQE:G
Ribosomal protein S82VQE:H
Ribosomal proteins L15p and L18e1VQO:L,2J01:P
Ribosomal proteins S24e, L23 and L15e1VQO:S,1VQO:M
Ribosome and ribosomal fragments2VQE:L,2VQE:O,2VQE:P,2VQE:S,2VQE:E
S-adenosyl-L-methionine-dependent methyltransferases1AV6:A,2BH2:A
S13-like H2TH domain2VQE:M
SRP191JID:A
Signal peptide-binding domain1HQ1:A
Sm-like ribonucleoproteins1KQ2:A,1M8V:A
TGS-like1QF6:A
TROVE domain-like1YVP:A
ThrRS/AlaRS common domain1QF6:A
Tombusvirus P19 core protein, VP191R9F:A
Translation proteins1B23:P,1VQO:B,2J01:E
Translation proteins SH3-like domain1VQO:T,1VQO:Q,1VQO:A,2J01:T
Translational machinery components1VQO:N,2VQE:K
ValRS/IleRS/LeuRS editing domain1FFY:A
Zn-binding ribosomal proteins1VQO:Z,1VQO:3,2J01:5
dsRNA-binding domain-like2NUG:A
p53-like transcription factors1OOA:A
tRNA-binding arm1SER:A
tRNA-guanine transglycosylase1Q2R:A
tRNA-intron endonuclease catalytic domain-like2GJW:A
vWA-like1YVP: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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