Used review papers for tool gathering
- Zhang 2019 https://doi.org/10.1093/bib/bbx168
- Yan 2016 https://doi.org/10.1093/bib/bbv023
- Corley 2020 https://doi.org/10.1016/j.molcel.2020.03.011
- Marchese 2016 https://doi.org/10.1002/wrna.1378
- Pan 2019 https://doi.org/10.1002/wrna.1544
- Wei 2022 https://doi.org/10.1093/bib/bbab540
- Miao 2015 https://doi.org/10.1371/journal.pcbi.1004639
Available prediction tools
| Tool | Reference | Year | Citations
(Google Scholar, Sep 2024) |
Link & format | Accessibility & licensing | Input | Prediction output | Notes |
| RPISeq | Muppirala et al. | 2011 | 486 | http://pridb.gdcb.iastate.edu/RPISeq/
web server |
freeware | RNA and protein sequence | score result (interaction probability) | |
| XRPI | Jain et al. | 2018 | 22 | https://universe.bits-pilani.ac.in/goa/aduri/xRPI
stand alone web server |
freeware | RNA and protein sequence | score result (interaction probability) | |
| PLIP | Adasme et al. | 2021 | 1026 (1842 on previous publication from 2015) | https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index
stand alone and web server |
freeware, GPL-2.0 license | determined 3D structure / PDB file | interacting residues of RNA and protein in structural context (+ bond type) | |
| PRI Hotscore | Krüger et al. | 2018 | 73 | https://pri-hotscore.labs.vu.nl/main.php
web server |
freeware | determined 3D structure / PDB file of RP-complex | interacting residues of protein in structural context | |
| PredPRBA | Deng et al. | 2019 | 34 | http://predprba.denglab.org/
web server |
freeware | determined 3D structure / PDB file | predicted binding free energy (ΔG) between protein and RNA chain of PDB complex | gradient boosting regression tree models with learned features from protein and RNA sequence and structure (data set) |
| NucleicNet | Lam et al. | 2019 | 95 | http://www.cbrc.kaust.edu.sa/NucleicNet/
web server https://github.com/jhmlam/NucleicNet/ stand alone |
freeware, AGPL-3.0 license | determined 3D structure / PDB file (protein or both) | protein surface analysis:
Pymol session with top binding sites for RNA chains logo: weblogo of RNA-protein complex |
|
| PRIdictor | Tuvshinjargal et al. | 2016 | 56 | http://www.rnainter.org/PRIdictor/
web server http://bclab.inha.ac.kr/pridictor/usage.html web application |
freeware | RNA and protein sequence | interaction probability per residue for RNA and protein | |
| RsiteDB | Shulman-Peleg et al. | 2008 | 52 | http://bioinfo3d.cs.tau.ac.il/rsitedb/rsite_about.html
web server |
freeware | determined 3D structure / PDB file | binding sites (based on other similar proteins) | based on human/model organisms; only a limited dataset of PDB entries are covered |
| catRAPID | Agostini et al. | 2013 | 272 | http://service.tartaglialab.com/update_submission/423433/0cd5163900
web server |
freeware, CC BY-NC-SA 4.0 | RNA and protein sequence | interaction probability per residue for RNA and protein (as heatmap) | trained on model organisms/human |
| PRince | Barik et al. | 2012 | 23 | http://www.facweb.iitkgp.ac.in/~rbahadur/prince/home.html
web server |
freeware | determined 3D structure / PDB file | lists (in PDB format) interface atoms for both protein and RNA chain + output parameters | |
| hybridNAP | Zhang et al. | 2019 | 111 | http://biomine.cs.vcu.edu/servers/hybridNAP/
web server |
freeware, non-commercial | protein sequence | csv with propensity per amino acid to bind nucleic acids or protein (+ visualization in browser) | |
| GraphProt | Maticzka et al. | 2014 | 273 | https://github.com/dmaticzka/GraphProt
http://www.bioinf.uni-freiburg.de/Software/GraphProt stand alone |
freeware, MIT license | experimental datasets; RNA sequence | binding site motifs for RNA sequence and secondary structure elements | experimental dataset (RNAcompete, CLIP-Seq; self-supplied) with bound and unbound RBPs, included RNA secondary structure |
| HOCNNLB | Zhang et al. | 2019 | 20 | https://github.com/NWPU-903PR/HOCNNLB
stand alone |
freeware, non-commercial | lncRNA sequence dataset | binding site for RBP on lncRNA sequences | higher-order nucleotide encoding convolutional neural network-based method |
| BERT-RBP | Yamada & Hamada | 2022 | 31 | https://github.com/kkyamada/bert-rbp
stand alone |
freeware | CLIP dataset (RNA sequences) | RBP-binding property of RNA sequences (yes or no) | data-trained model, analyses transcript region type, RNA secondary structure elements and binding motifs |
| PredRBR | Tang et al. | 2017 | 43 | http://denglab.org/PredRBR/
stand alone |
freeware | determined 3D structure / PDB file (has to cover both protein and RNA) | predicts RNA-binding residues in the protein structure | sequential and spatial features are included in the model; older idea from PredPRBA people |
| PRIME3D2D | Xie et al. | 2020 | 14 | http://www.rnabinding.com/PRIME-3D2D/
web server |
freeware | determined 3D structure / PDB file for protein and RNA each | nucleotides predicted as binding site for the protein get labeled with “+” | structures used, RNA is “reduced” to secondary structure information |
| aPRBind | Liu et al. | 2021 | 23 | https://github.com/ChunhuaLiLab/aPRbind
stand alone |
freeware | protein sequence | RNA-binding residues in protein structure model | CNN model with sequence features, evolutionary information, residue properties & propensities (from protein structure model) |
| RBPPred | Zhang & Liu | 2017 | 95 | http://rnabinding.com/RBPPred.html
stand alone |
freeware | protein sequence(s) | predicts whether the protein binds RNAs in general (probability) | model based on evolutionary information and physicochemical properties of proteins, SVM classifier |
| RCK | Orenstein et al. | 2016 | 79 | http://rck.csail.mit.edu/
stand alone |
freeware | RPI dataset: set of RNA sequences with estimated binding affinities + RNA secondary structure annotations of sequences | RNA-protein motif preference (for short RNA transcripts each a binding “intensity” is given) | trained on RNAcompete experimental data; k-mer model with local secondary structure preferences; extension to RNAcontext (adding k-mer approach) |
| MEME | Bailey et al. | 2015 | 3255 | https://meme-suite.org/meme/tools/meme
web server and stand alone |
freeware, limited non-commercial use license | (one or) multiple sequences where common motif should be found | motif with weblogo and position in sequence (DNA, RNA, protein) | not necessarily interaction related
add-on: MEMERIS |
| DRNApred | Yan & Kurgan | 2017 | 204 | http://biomine.cs.vcu.edu/servers/DRNApred/
web server |
freeware, non-commercial | protein sequence | txt file with interaction probability for DNA/RNA per amino acid | |
| COACH | Yang et al. | 2013 | 974 | https://zhanggroup.org/COACH/
web server |
freeware | determined 3D structure / PDB file or protein sequence | binding site recognition based on homologous template structures | further versions:
COACH-D https://doi.org/10.1093/nar/gky439 NucBind |
| aaRNA | Li et al. | 2014 | 74 | http://sysimm.ifrec.osaka-u.ac.jp/aarna/
web server |
freeware | determined 3D structure / PDB file or protein sequence | binary propensity and di-nucleotide propensity of each residue (amino acid) to bind RNA in general, also structural visualization | neural network trained on RNA-RBP-complex datasets |
| Deepnet-RBP | Zhang et al. | 2015 | 301 | https://github.com/thucombio/deepnet-rbp
stand alone |
freeware, limited use license | CLIP dataset (RNA sequences) | RNA sequence and 3D structure motifs for RBP binding site preferences | multimodal deep learning model based on experimentally identified RBP binding sites (CLIP-seq) |
| DeepBoost | Li et al. | 2017 | 22 | http://github.com/dongfanghong/deepboost
stand alone |
freeware | RNA-protein data set (experimental) | binding site preferences | |
| DeepSite | Jiménez et al. | 2017 | 582 | https://playmolecule.com/deepsite/
web server |
freeware | determined 3D structure / PDB file | binding site/pocket (highlighted in spatial structure) | general ligand binding site prediction, not exclusively RNA |
| SSMART | Munteanu et al. | 2018 | 23 | https://ohlerlab.mdc-berlin.de/software/SSMART_137/
stand alone |
freeware | RNA-protein data set (experimental) | RNA motif (weblogo) | RNA motif finder in RBP |
| ThermoNet | Su et al. | 2019 | 25 | https://github.com/suyufeng/ThermoNet
stand alone |
freeware, limited use license | CLIP dataset (RNA sequences) | binding intensity for the RNA | sequence - (k-mer-)embedding convolutional neural network + thermodynamics of secondary structures |
| iCapsule | Shen et al. | 2019 | 25 | https://github.com/naturomics/CapsNet-Tensorflow
stand alone |
freeware, Apache-2.0 license | RNA-protein data set (experimental) | motif (weblogo) | based on multiple modifications of Capsnet |
| ProbeRating | Yang et al. | 2020 | 8 | https://github.com/syang11/ProbeRating
stand alone |
freeware, MIT license | RNA-protein data set | binding profiles for RBPs | |
| RPI-Net | Yan et al. | 2020 | 40 | https://github.com/HarveyYan/RNAonGraph
stand alone |
freeware, MIT license | CLIP dataset (RNA sequences) | RNA secondary structure models and motifs | |
| GraphBind | Xia et al. | 2021 | 87 | http://www.csbio.sjtu.edu.cn/bioinf/GraphBind/
web server and stand alone |
freeware, GPLv3.0, CC BY 4.0 | determined 3D structure / PDB file (protein) | identify RNA-binding residues in protein (highlighted in protein structure on website, csv file to download) | |
| DeepCLIP | Grønning et al. | 2020 | 83 | http://deepclip.compbio.sdu.dk
web server https://github.com/deepclip/deepclip stand alone |
freeware, MIT license | CLIP datasets; RNA sequence | binding profiles and motifs for RNA sequence (i.e. potential binding sites) | pre-trained models based on experimental datasets (CLIP-Seq, iCLIP, etc) |
| PrismNet | Sun et al. | 2021 | 86 | http://prismnet.zhanglab.net/
web server https://github.com/kuixu/PrismNet stand alone |
freeware, MIT license | RNA-protein data set (experimental) | predict dynamic RBP binding across sequence, motif visualization | |
| iDeepS | Pan et al. | 2018 | 249 | https://github.com/xypan1232/iDeepS
stand alone |
freeware, CC0 1.0 | RNA-protein data set (experimental) / RNA sequence (prediction) | binding site motif | previous version: iDeepE https://doi.org/10.1093/bioinformatics/bty364 |
| 3dRPC | Huang et al. | 2013 | 71 | http://biophy.hust.edu.cn/new/3dRPC/create
web server |
freeware, non-commercial | determined 3D structure / PDB file for protein and RNA each | RNA and protein docking to a complex + scoring | dock RNA and protein structure |
| KYG | Kim et al. | 2006 | 147 | http://cib.cf.ocha.ac.jp/KYG/
web server |
freeware | determined 3D structure / PDB file (protein) + MSA (depending on used method) | RNA interface residue prediction | |
| OPRA | Pérez-Cano & Fernández-Recio | 2009 | 106 | https://life.bsc.es/pid/opra/default/index
web server |
freeware, academic access only | determined 3D structure / PDB file | binding potential per residue (protein) to bind RNA (annotated pdb file and score result file) | |
| RBPmap | Paz et al. | 2014 | 510 | http://rbpmap.technion.ac.il/index.html
web server and stand alone |
freeware | RNA sequence(s) and an RBP motif | RBP-binding motifs in RNA (potential binding sites for RBP) | |
| IPMiner | Pan et al. | 2016 | 138 | https://github.com/xypan1232/IPMiner
stand alone |
freeware, CC0 1.0 | RNA-protein dataset; RNA and protein sequences | interaction score for RNA and protein | |
| DLPRB | Ben-Bassat et al. | 2018 | 87 | https://github.com/ilanbb/dlprb
stand alone |
freeware, MIT license | RNA-protein dataset (experimental), i.e.: RNA sequence file with binding affinity + file with structural information (vector of 5 possible structural elements for each position) | binding site preference visualized as RNA sequence and structure logos | CNN |
| ssHMM | Heller et al. | 2017 | 40 | https://github.molgen.mpg.de/heller/ssHMM
stand alone |
freeware, GPL-3.0 license | RNA-binding protein data (e.g. CLIP-Seq) | sequence - structure motifs/preferences of RNAs (for the RBPs) as a graph | hidden Markov model (HMM) with Gibbs sampling |
| beRBP | Yu et al. | 2019 | 39 | http://bioinfo.vanderbilt.edu/beRBP/predict.html | freeware | RNA sequence(s) + PWM or sequence of RBP | RBP-binding sites/motifs in RNA sequence | limited to a trained selection of human RBPs |
Unavailable prediction tools
| Tool | Reference | Year | Tool link | Info |
| RPIFSE | Wang et al. | 2019 | - | not accessible / no link available |
| DeepRKE | Deng et al. | 2019 | - | not accessible / no link available |
| RPI-SAN | Yi et al. | 2018 | - | not accessible / no link available |
| CTF / CGR | Wang & Wu | 2018 | - | not accessible / no link available |
| ELM | Wang et al. | 2018 | - | not accessible / no link available |
| LGBM | Zhan et al. | 2018 | - | not accessible / no link available |
| Oli | Livi & Blanzieri | 2014 | - | not accessible / no link available |
| ProteRNA | Huang et al. | 2010 | - | not accessible / no link available |
| RNAProB | Cheng et al. | 2008 | - | not accessible / no link available |
| Struct-NB | Towfic et al. | 2010 | - | not accessible / no link available |
| RNAcontext | Kazan et al. | 2010 | http://morrislab.med.utoronto.ca/software | not maintained / accessible anymore |
| RNAcommender | Corrado et al. | 2016 | http://rnacommender.disi.unitn.it/ | not maintained / accessible anymore |
| lncPRO | Lu et al. | 2013 | http://bioinfo.bjmu.edu.cn/lncpro/ | not maintained / accessible anymore |
| CFRP | Dai et al. | 2019 | http://www.dailab.cn/CFRP/index.html | not maintained / accessible anymore |
| RPiRLS | Shen et al. | 2018 | http://bmc.med.stu.edu.cn/RPiRLS | not maintained / accessible anymore |
| RPI-Bind | Luo et al. | 2017 | http://ctsb.is.wfubmc.edu/publications/RPI-Bind-Pred.php | not maintained / accessible anymore |
| RNAProSite | Sun et al. | 2016 | http://lilab.ecust.edu.cn/NABind | not maintained / accessible anymore |
| rpiCOOL | Akbaripour-Elahabad et al. | 2016 | http://biocool.ir/rpicool.html | not maintained / accessible anymore |
| RPI-Pred | Suresh et al. | 2015 | http://ctsb.is.wfubmc.edu/projects/rpi-pred | not maintained / accessible anymore |
| DeepBind | Alipanahi et al. | 2015 | http://tools.genes.toronto.edu/deepbind/ | not maintained / accessible anymore |
| PRIPU | Cheng et al. | 2015 | http://admis.fudan.edu.cn/projects/pripu.htm | not maintained / accessible anymore |
| RBscore | Miao & Westhof | 2015 | http://ahsoka.u-strasbg.fr/rbscore/ | not maintained / accessible anymore |
| RBRIdent | Xiong et al. | 2015 | http://166.111.152.91/RBRIdent | not maintained / accessible anymore |
| RNABindRPlus | Walia et al. | 2014 | http://einstein.cs.iastate.edu/RNABindRPlus/ | not maintained / accessible anymore |
| RBRDetector | Yang et al. | 2014 | http://ibi.hzau.edu.cn/rbrdetector | not maintained / accessible anymore |
| SRCpred | Fernandez et al. | 2011 | http://tardis.nibio.go.jp/netasa/srcpred | not maintained / accessible anymore |
| DRNA / SPOT | Zhao et al. | 2011 | http://sparks.informatics.iupui.edu/spot | not maintained / accessible anymore |
| Predict_RBP | Wang et al. | 2010 | http://cic.scu.edu.cn/bioinformatics/Predict_RBP.rar | not maintained / accessible anymore |
| NAPS | Carson et al. | 2010 | http://proteomics.bioengr.uic.edu/NAPS | not maintained / accessible anymore |
| PiRaNhA | Murakami et al. | 2010 | http://www.bioinformatics.sussex.ac.uk/PIRANHA | not maintained / accessible anymore |
| BindN+ | Wang et al. | 2010 | http://bioinfo.ggc.org/bindn+/ | not maintained / accessible anymore |
| PRBR | Ma et al. | 2010 | http://www.cbi.seu.edu.cn/PRBR/ | not maintained / accessible anymore |
| PRNA | Liu et al. | 2010 | http://www.aporc.org/doc/wiki/PRNA | not maintained / accessible anymore |
| PRIP | Maetschke & Yuan | 2009 | https://qfab.org/PRIP | not maintained / accessible anymore |
| PRINTR | Wang et al. | 2008 | http://210.42.106.80/printr/ | not maintained / accessible anymore |
| RISP | Tong et al. | 2008 | http://grc.seu.edu.cn/RISP | not maintained / accessible anymore |
| Pprint | Kumar et al. | 2007 | http://www.imtech.res.in/raghava/pprint/ | not maintained / accessible anymore |
| DBS-Pred | Ahmad et al. | 2004 | http://www.netasa.org/dbs-pred/ | not maintained / accessible anymore |
| DR_bind1 | Chen et al. | 2014 | https://drbind.limlab.ibms.sinica.edu.tw/ | tool does not perform |