Protein aggregation predictors
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| Method | Last Update | Acess (Web server/downloadable) | Principle | Input | Output | Links | |
|---|---|---|---|---|---|---|---|
| Files | Parameters | ||||||
| Amyloidogenic pattern | 2004 | AmylPred | Structure-related | sequence | - | Amyloidogenic regions | http://aias.biol.uoa.gr/AMYLPRED2/ |
| TANGO | 2004 | web server/AmylPred | Phenomenological | sequence | pH/ionic strength | Overall aggregation and amyloidoidogenic regions | http://tango.crg.es/ |
| 3D Profile (Zipper DB) | 2006 | web server | Structure-related | sequence | - | Amyloidogenic regions and, energy and beta-sheet conformation | http://services.mbi.ucla.edu/zipperdb/submit |
| Average Packing Density | 2006 | AmylPred | Structure-related | sequence | - | Amyloidogenic regions | http://aias.biol.uoa.gr/AMYLPRED2/ |
| Beta-strand contiguity | 2007 | AmylPred | Phenomenological | sequence | - | beta-strand formation | http://aias.biol.uoa.gr/AMYLPRED2/ |
| Hexapeptide Conformational Energy /Pre-amyl | 2007 | AmylPred | Structure-related | sequence | - | Amyloidogenic regions and energy | http://aias.biol.uoa.gr/AMYLPRED2/ |
| CamSol intrinsic (Zyggregator) | 2017 | web server | Phenomenological | sequence | pH | Calculation of the overall intrinsic solubility score and solubility profile | http://www-mvsoftware.ch.cam.ac.uk/ |
| AGGRESCAN | 2007 | web server/AmylPred | Phenomenological | sequence | - | Overall aggregation and amyloidogenic regions | http://bioinf.uab.es/aggrescan/ http://aias.biol.uoa.gr/AMYLPRED2/ |
| SALSA | 2007 | Metamyl | Phenomenological | sequence | hot spot lenght | Amyloidogenic regions | http://amypdb.genouest.org/e107_plugins/amypdb_aggregation/db_prediction_salsa.php |
| Pafig | 2009 | downloable/AmylPred/Metamyl | Phenomenological | sequence | - | Amyloidogenic regions | http://aias.biol.uoa.gr/AMYLPRED2/ |
| Net-CSSP | 2009 | web server/AmylPred | Structure-related | sequence/pdb | single/dual network-treshold | Amyloidogenic propensity regions | http://cssp2.sookmyung.ac.kr/ http://aias.biol.uoa.gr/AMYLPRED2/ |
| PAGE | 2009 | - | Structure-related | sequence | - | Generic or beta-aggregation prone regions | |
| Betascan | 2009 | web server/downloadable | Structure-related | sequence | length | Amyloidogenic regions | http://betascan.csail.mit.edu. |
| SAP | 2009 | - | 3D structure | pdb file | - | Dynamic exposed hydrophobic pathces | |
| FoldAmyloid | 2010 | web server/Metamyl | Structure-related | sequence | scale, treshold, averaging frame | Amyloidogenic regions | http://bioinfo.protres.ru/fold-amyloid/ |
| Waltz | 2010 | web server/AmylPred/Metamyl | Structure-related | sequence | pH, specificity, sensitivity | Amyloidogenic regions | http://waltz.switchlab.org/ http://aias.biol.uoa.gr/AMYLPRED2/ |
| STITCHER | 2012 | - | Structure-related | sequence | - | Amyloidogenic regions | http://stitcher.csail.mit.edu/ |
| MetAmyl | 2013 | web server | Consensus method | sequence | treshold | Overall generic and amyloidogenic regions based on the consensus | http://metamyl.genouest.org/e107_plugins/metamyl_aggregation/db_prediction_meta.php |
| AmylPred2 | 2013 | web server | Consensus method | sequence | - | Overall generic and amyloidogenic regions based on the consensus | http://aias.biol.uoa.gr/AMYLPRED2/ |
| PASTA 2.0 | 2014 | web server/downloadable | Structure-related | sequence | top pairings and energies, mutations and protein-protein | Amyloidogenic regions, energy, and beta-sheet orientation in aggregates | http://protein.bio.unipd.it/pasta2/index.html |
| FISH Amyloid | 2014 | web server/downloadable | Structure-related | sequence | treshold | Amyloidogenic regions | http://comprec-lin.iiar.pwr.edu.pl/fishInput/ |
| GAP | 2014 | web server | Structure-related | sequence | - | Overall aggregation and amyloidogenic regions | https://www.iitm.ac.in/bioinfo/GAP/ |
| APPNN | 2015 | downloable | Phenomenological | sequence | - | Amyloidogenic regions | https://CRAN.R-project.org/package=appnn |
| ArchCandy | 2015 | downloable | Structure-related | sequence | - | Amyloidogenic regions | https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=7 |
| Amyload | 2015 | web server | Consensus method | sequence | - | Overall generic and amyloidogenic regions | http://comprec-lin.iiar.pwr.edu.pl/amyload/analysisPage/ |
| CamSol Structurally Corrected | 2015 | webserver | 3D structure | pdb file | pH, patch radius | Exposed aggregation-prone patches and mutated variants design | http://www-mvsoftware.ch.cam.ac.uk/index.php/login |
| Solubis | 2016 | web server | 3D structure | pdb file | chain, treshold, gatekeeper | Aggregation propensity and stability vs mutations | http://solubis.switchlab.org/node/add/solubis-job |
| AmyloGram | 2017 | web server | Phenomenological | sequence | - | Overall aggregation and amyloidogenic regions | http://www.smorfland.uni.wroc.pl/shiny/AmyloGram/ |
| AggScore | 2018 | downloable | Structure-related | sequence | - | Amyloidogenic regions | |
| AGGRESCAN 3D 2.0 | 2019 | web server | 3D structure | pdb file | dynamic mode, mutations, patch radius, stability, enhance solubility | Dynamic exposed aggregation-prone patches and mutated variants design | http://biocomp.chem.uw.edu.pl/A3D2/ |