Table 1.
Some computational resources for predicting amyloidogenic regions in proteins.
| Program | Comments and/or URL | Reference |
|---|---|---|
| AggreProt | Webserver for predicting amyloid-prone regions promoting protein aggregation https://loschmidt.chemi.muni.cz/aggreprot/ (accessed on 1 October 2024) |
[92] |
| Aggrescan | http://bioinf.uab.es/aggrescan/ (accessed on 1 October 2024) | [93] |
| https://biocomp.chem.uw.edu.pl/A3D/ (accessed on 1 October 2024) | [94] | |
| https://biocomp.chem.uw.edu.pl/a4d/ (accessed on 1 October 2024) | [95] | |
| AMYGNN | Seemingly no online server. Database reconstructable via https://github.com/yzjizwz/AMYGNN.git (accessed on 1 October 2024) | [96] |
| AmyLoad | Database and server for amyloidogenic sequences https://comprec-lin.iiar.pwr.edu.pl/amyload/ (accessed on 1 October 2024) | [97] |
| AmyloComp | Predicts co-aggregation of two proteins within an amyloid fibril https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=30 (accessed on 1 October 2024) | [98] |
| Amylogram | http://biongram.biotech.uni.wroc.pl/AmyloGram/ (accessed on 1 October 2024) Amyloidogenicity is strongly correlated with hydrophobicity, a tendency to form β-sheets, and lower flexibility of amino acid residues | [74,99] |
| AmyloGraph | Database of amyloid–amyloid interactions https://amylograph.com/ (accessed on 1 October 2024) | [87] |
| AMYPred-FRL | http://pmlabstack.pythonanywhere.com/AMYPred-FRL (accessed on 1 October 2024) | [100] |
| AmyPro | Database of validated amyloidogenic regions in proteins. http://amypro.net/ (accessed on 1 October 2024) | [101] |
| ArchCandy | https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=32 (accessed on 1 October 2024) | [102,103] |
| AnuPP | Aggregation Nucleation Prediction in Peptides and Proteins https://web.iitm.ac.in/bioinfo2/ANuPP/homeseq1/ (accessed on 1 October 2024) | [104] |
| Betascan | http://cb.csail.mit.edu/cb/betascan/betascan.html (accessed on 1 October 2024) | [105] |
| Beta-serpentine | http://bioinfo.montp.cnrs.fr/index.php?%20r=b-serpentine (accessed on 1 October 2024) | [106] |
| Bydapest amyloid predictor | Works on hexapeptides. https://pitgroup.org/bap/ (accessed on 1 October 2024) | [107] |
| Cordax | https://cordax.switchlab.org/ (accessed on 1 October 2024) | [108] |
| CPAD | Curated protein aggregation database https://www.iitm.ac.in/bioinfo/CPAD/ (accessed on 1 October 2024) | [109] |
| ENTAIL | “yEt aNoTher Amyloid fIbrILs cLassifier”. Code at https://github.com/luigidibiasi/ENTAIL (accessed on 1 October 2024) | [110] |
| FISH Amyloid | https://comprec-lin.iiar.pwr.edu.pl/ (accessed on 1 October 2024) | [111] |
| FoldAmyloid | http://bioinfo.protres.ru/fold-amyloid/ (accessed on 1 October 2024) | [112] |
| GAP | Generalised aggregation proneness https://www.iitm.ac.in/bioinfo/GAP/ (accessed on 1 October 2024) | [113] |
| MILAMP | “Multiple Instance Prediction of Amyloid Proteins”. Links to server and code are to be found at http://faculty.pieas.edu.pk/fayyaz/software.html#MILAMP (accessed on 1 October 2024) | [114] |
| PACT | Prediction of amyloid cross-interaction by threading https://pact.e-science.pl/pact/ (accessed on 1 October 2024) | [115] |
| PAPA and TANGO | Not clear if still available online | [116] |
| Pasta 2.0 | http://old.protein.bio.unipd.it/pasta2/ (accessed on 1 October 2024) | [117] |
| ReRF-Pred | Stated as http://106.12.83.135:8080/ReRF-Pred/ (accessed on 1 October 2024) but seemingly inaccessible presently | [118] |
| RFAmyloid | Said to be at http://server.malab.cn/RFAmyloid/ (accessed on 1 October 2024) | [119] |
| Tango | Aggregating regions in unfolded protein chains http://tango.crg.es/. (accessed on 1 October 2024) Needs account | [116] |
| TAPASS | https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=32 (accessed on 1 October 2024) | [103] |
| WALTZ | https://waltz.switchlab.org/ (accessed on 1 October 2024) | [120] |
| WALTZDB | Database | [86] |
| WALTZ-DB 2.0 | [121] | |
| ZipperDB | https://zipperdb.mbi.ucla.edu/ (accessed on 1 October 2024) | [122] |