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== List of Protein aggregation predictors ==
== List of Protein aggregation predictors ==
Computational methods that use protein sequence and/ or protein structure to predict [[protein aggregation]]. The table below, shows the main features of software for prediction of protein aggregation
Computational methods that use protein sequence and/ or protein structure to predict [[protein aggregation]]. The table below, shows the main features of software for prediction of protein aggregation
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!Additional parameters
!Additional parameters
|-
|-
|'''Amyloidogenic Patten'''<ref>{{Cite journal|last=Paz|first=Manuela López de la|last2=Serrano|first2=Luis|date=2004-01-06|title=Sequence determinants of amyloid fibril formation|url=https://www.pnas.org/content/101/1/87|journal=Proceedings of the National Academy of Sciences|language=en|volume=101|issue=1|pages=87–92|doi=10.1073/pnas.2634884100|issn=0027-8424|pmc=PMC314143|pmid=14691246}}</ref>
|'''Amyloidogenic Patten'''<ref>{{Cite journal|last=Paz|first=Manuela López de la|last2=Serrano|first2=Luis|date=2004-01-06|title=Sequence determinants of amyloid fibril formation|url=https://www.pnas.org/content/101/1/87|journal=Proceedings of the National Academy of Sciences|language=en|volume=101|issue=1|pages=87–92|doi=10.1073/pnas.2634884100|issn=0027-8424|pmc=314143|pmid=14691246}}</ref>
|2004
|2004
|Web Server- [http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Web Server- [http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''Tango''' <ref>{{Cite journal|last=Rousseau|first=F|last2=Schymkowitz|first2=J|last3=Serrano|first3=L|date=2006-02|title=Protein aggregation and amyloidosis: confusion of the kinds?|url=https://linkinghub.elsevier.com/retrieve/pii/S0959440X06000121|journal=Current Opinion in Structural Biology|language=en|volume=16|issue=1|pages=118–126|doi=10.1016/j.sbi.2006.01.011}}</ref><ref>{{Cite journal|last=Fernandez-Escamilla|first=Ana-Maria|last2=Rousseau|first2=Frederic|last3=Schymkowitz|first3=Joost|last4=Serrano|first4=Luis|date=2004-10|title=Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins|url=http://www.nature.com/articles/nbt1012|journal=Nature Biotechnology|language=en|volume=22|issue=10|pages=1302–1306|doi=10.1038/nbt1012|issn=1087-0156}}</ref><ref>{{Cite journal|last=Linding|first=Rune|last2=Schymkowitz|first2=Joost|last3=Rousseau|first3=Frederic|last4=Diella|first4=Francesca|last5=Serrano|first5=Luis|date=2004-09|title=A Comparative Study of the Relationship Between Protein Structure and β-Aggregation in Globular and Intrinsically Disordered Proteins|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283604007715|journal=Journal of Molecular Biology|language=en|volume=342|issue=1|pages=345–353|doi=10.1016/j.jmb.2004.06.088}}</ref>
|'''Tango''' <ref>{{Cite journal|last=Rousseau|first=F|last2=Schymkowitz|first2=J|last3=Serrano|first3=L|date=February 2006|title=Protein aggregation and amyloidosis: confusion of the kinds?|url=https://linkinghub.elsevier.com/retrieve/pii/S0959440X06000121|journal=Current Opinion in Structural Biology|language=en|volume=16|issue=1|pages=118–126|doi=10.1016/j.sbi.2006.01.011}}</ref><ref>{{Cite journal|last=Fernandez-Escamilla|first=Ana-Maria|last2=Rousseau|first2=Frederic|last3=Schymkowitz|first3=Joost|last4=Serrano|first4=Luis|date=October 2004|title=Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins|url=http://www.nature.com/articles/nbt1012|journal=Nature Biotechnology|language=en|volume=22|issue=10|pages=1302–1306|doi=10.1038/nbt1012|issn=1087-0156}}</ref><ref>{{Cite journal|last=Linding|first=Rune|last2=Schymkowitz|first2=Joost|last3=Rousseau|first3=Frederic|last4=Diella|first4=Francesca|last5=Serrano|first5=Luis|date=September 2004|title=A Comparative Study of the Relationship Between Protein Structure and β-Aggregation in Globular and Intrinsically Disordered Proteins|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283604007715|journal=Journal of Molecular Biology|language=en|volume=342|issue=1|pages=345–353|doi=10.1016/j.jmb.2004.06.088}}</ref>
|2004
|2004
|Web Server-[http://tango.crg.es/ TANGO]
|Web Server-[http://tango.crg.es/ TANGO]
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|Overall aggregation and amyloidoidogenic regions
|Overall aggregation and amyloidoidogenic regions
|-
|-
|'''Zipper DB''' <ref>{{Cite journal|last=Thompson|first=Michael J.|last2=Sievers|first2=Stuart A.|last3=Karanicolas|first3=John|last4=Ivanova|first4=Magdalena I.|last5=Baker|first5=David|last6=Eisenberg|first6=David|date=2006-03-14|title=The 3D profile method for identifying fibril-forming segments of proteins|url=https://www.pnas.org/content/103/11/4074|journal=Proceedings of the National Academy of Sciences|language=en|volume=103|issue=11|pages=4074–4078|doi=10.1073/pnas.0511295103|issn=0027-8424|pmc=PMC1449648|pmid=16537487}}</ref><ref>{{Cite journal|last=Nelson|first=Rebecca|last2=Sawaya|first2=Michael R.|last3=Balbirnie|first3=Melinda|last4=Madsen|first4=Anders Ø|last5=Riekel|first5=Christian|last6=Grothe|first6=Robert|last7=Eisenberg|first7=David|date=2005-06|title=Structure of the cross-β spine of amyloid-like fibrils|url=https://www.nature.com/articles/nature03680|journal=Nature|language=en|volume=435|issue=7043|pages=773–778|doi=10.1038/nature03680|issn=1476-4687|pmc=PMC1479801|pmid=15944695}}</ref><ref>{{Cite journal|last=Kuhlman|first=Brian|last2=Baker|first2=David|date=2000-09-12|title=Native protein sequences are close to optimal for their structures|url=https://www.pnas.org/content/97/19/10383|journal=Proceedings of the National Academy of Sciences|language=en|volume=97|issue=19|pages=10383–10388|doi=10.1073/pnas.97.19.10383|issn=0027-8424|pmc=PMC27033|pmid=10984534}}</ref><ref>{{Cite journal|last=Sawaya|first=Michael R.|last2=Sambashivan|first2=Shilpa|last3=Nelson|first3=Rebecca|last4=Ivanova|first4=Magdalena I.|last5=Sievers|first5=Stuart A.|last6=Apostol|first6=Marcin I.|last7=Thompson|first7=Michael J.|last8=Balbirnie|first8=Melinda|last9=Wiltzius|first9=Jed J. W.|last10=McFarlane|first10=Heather T.|last11=Madsen|first11=Anders Ø.|date=2007-05|title=Atomic structures of amyloid cross-β spines reveal varied steric zippers|url=http://www.nature.com/articles/nature05695|journal=Nature|language=en|volume=447|issue=7143|pages=453–457|doi=10.1038/nature05695|issn=0028-0836}}</ref>
|'''Zipper DB''' <ref>{{Cite journal|last=Thompson|first=Michael J.|last2=Sievers|first2=Stuart A.|last3=Karanicolas|first3=John|last4=Ivanova|first4=Magdalena I.|last5=Baker|first5=David|last6=Eisenberg|first6=David|date=2006-03-14|title=The 3D profile method for identifying fibril-forming segments of proteins|url=https://www.pnas.org/content/103/11/4074|journal=Proceedings of the National Academy of Sciences|language=en|volume=103|issue=11|pages=4074–4078|doi=10.1073/pnas.0511295103|issn=0027-8424|pmc=1449648|pmid=16537487}}</ref><ref>{{Cite journal|last=Nelson|first=Rebecca|last2=Sawaya|first2=Michael R.|last3=Balbirnie|first3=Melinda|last4=Madsen|first4=Anders Ø|last5=Riekel|first5=Christian|last6=Grothe|first6=Robert|last7=Eisenberg|first7=David|date=June 2005|title=Structure of the cross-β spine of amyloid-like fibrils|url=https://www.nature.com/articles/nature03680|journal=Nature|language=en|volume=435|issue=7043|pages=773–778|doi=10.1038/nature03680|issn=1476-4687|pmc=1479801|pmid=15944695}}</ref><ref>{{Cite journal|last=Kuhlman|first=Brian|last2=Baker|first2=David|date=2000-09-12|title=Native protein sequences are close to optimal for their structures|url=https://www.pnas.org/content/97/19/10383|journal=Proceedings of the National Academy of Sciences|language=en|volume=97|issue=19|pages=10383–10388|doi=10.1073/pnas.97.19.10383|issn=0027-8424|pmc=27033|pmid=10984534}}</ref><ref>{{Cite journal|last=Sawaya|first=Michael R.|last2=Sambashivan|first2=Shilpa|last3=Nelson|first3=Rebecca|last4=Ivanova|first4=Magdalena I.|last5=Sievers|first5=Stuart A.|last6=Apostol|first6=Marcin I.|last7=Thompson|first7=Michael J.|last8=Balbirnie|first8=Melinda|last9=Wiltzius|first9=Jed J. W.|last10=McFarlane|first10=Heather T.|last11=Madsen|first11=Anders Ø.|date=May 2007|title=Atomic structures of amyloid cross-β spines reveal varied steric zippers|url=http://www.nature.com/articles/nature05695|journal=Nature|language=en|volume=447|issue=7143|pages=453–457|doi=10.1038/nature05695|issn=0028-0836}}</ref>
|2010
|2010
|Web Server- [http://services.mbi.ucla.edu/zipperdb/submit Zipper DB]
|Web Server- [http://services.mbi.ucla.edu/zipperdb/submit Zipper DB]
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|Amyloidogenic regions and, energy and beta-sheet conformation
|Amyloidogenic regions and, energy and beta-sheet conformation
|-
|-
|'''Average Packing Density'''<ref>{{Cite journal|last=Galzitskaya|first=Oxana V.|last2=Garbuzynskiy|first2=Sergiy O.|last3=Lobanov|first3=Michail Yurievich|date=2006-12-29|title=Prediction of Amyloidogenic and Disordered Regions in Protein Chains|url=https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020177|journal=PLOS Computational Biology|language=en|volume=2|issue=12|pages=e177|doi=10.1371/journal.pcbi.0020177|issn=1553-7358|pmc=PMC1761655|pmid=17196033}}</ref>
|'''Average Packing Density'''<ref>{{Cite journal|last=Galzitskaya|first=Oxana V.|last2=Garbuzynskiy|first2=Sergiy O.|last3=Lobanov|first3=Michail Yurievich|date=2006-12-29|title=Prediction of Amyloidogenic and Disordered Regions in Protein Chains|url=https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020177|journal=PLOS Computational Biology|language=en|volume=2|issue=12|pages=e177|doi=10.1371/journal.pcbi.0020177|issn=1553-7358|pmc=1761655|pmid=17196033}}</ref>
|2006
|2006
|Web Server-[http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Web Server-[http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''Beta-strand contiguity'''<ref>{{Cite journal|last=Zibaee|first=Shahin|last2=Makin|first2=O. Sumner|last3=Goedert|first3=Michel|last4=Serpell|first4=Louise C.|date=2007-05|title=A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone|url=http://doi.wiley.com/10.1110/ps.062624507|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|pmc=PMC2206631|pmid=17456743}}</ref>
|'''Beta-strand contiguity'''<ref>{{Cite journal|last=Zibaee|first=Shahin|last2=Makin|first2=O. Sumner|last3=Goedert|first3=Michel|last4=Serpell|first4=Louise C.|date=May 2007|title=A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone|url=http://doi.wiley.com/10.1110/ps.062624507|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|pmc=2206631|pmid=17456743}}</ref>
|2007
|2007
|Web Server- [http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Web Server- [http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
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|Amyloidogenic regions and energy
|Amyloidogenic regions and energy
|-
|-
|'''CamSol intrinsic'''<ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Aprile|first2=Francesco A.|last3=Vendruscolo|first3=Michele|date=2015-01|title=The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283614005312|journal=Journal of Molecular Biology|language=en|volume=427|issue=2|pages=478–490|doi=10.1016/j.jmb.2014.09.026}}</ref><ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Amery|first2=Leanne|last3=Ekizoglou|first3=Sofia|last4=Vendruscolo|first4=Michele|last5=Popovic|first5=Bojana|date=2017-12|title=Rapid and accurate in silico solubility screening of a monoclonal antibody library|url=http://www.nature.com/articles/s41598-017-07800-w|journal=Scientific Reports|language=en|volume=7|issue=1|pages=8200|doi=10.1038/s41598-017-07800-w|issn=2045-2322}}</ref>
|'''CamSol intrinsic'''<ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Aprile|first2=Francesco A.|last3=Vendruscolo|first3=Michele|date=January 2015|title=The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283614005312|journal=Journal of Molecular Biology|language=en|volume=427|issue=2|pages=478–490|doi=10.1016/j.jmb.2014.09.026}}</ref><ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Amery|first2=Leanne|last3=Ekizoglou|first3=Sofia|last4=Vendruscolo|first4=Michele|last5=Popovic|first5=Bojana|date=December 2017|title=Rapid and accurate in silico solubility screening of a monoclonal antibody library|url=http://www.nature.com/articles/s41598-017-07800-w|journal=Scientific Reports|language=en|volume=7|issue=1|pages=8200|doi=10.1038/s41598-017-07800-w|issn=2045-2322}}</ref>
|2017
|2017
|Web Server- [https://www-cohsoftware.ch.cam.ac.uk/ Ch'''e'''mistry of Health]
|Web Server- [https://www-cohsoftware.ch.cam.ac.uk/ Ch'''e'''mistry of Health]
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|Calculation of the overall intrinsic solubility score and solubility profile
|Calculation of the overall intrinsic solubility score and solubility profile
|-
|-
|'''AGGRESCAN'''<ref>{{Cite journal|last=Conchillo-Solé|first=Oscar|last2=de Groot|first2=Natalia S.|last3=Avilés|first3=Francesc X.|last4=Vendrell|first4=Josep|last5=Daura|first5=Xavier|last6=Ventura|first6=Salvador|date=2007-02-27|title=AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides|url=https://doi.org/10.1186/1471-2105-8-65|journal=BMC Bioinformatics|volume=8|issue=1|pages=65|doi=10.1186/1471-2105-8-65|issn=1471-2105|pmc=PMC1828741|pmid=17324296}}</ref>
|'''AGGRESCAN'''<ref>{{Cite journal|last=Conchillo-Solé|first=Oscar|last2=de Groot|first2=Natalia S.|last3=Avilés|first3=Francesc X.|last4=Vendrell|first4=Josep|last5=Daura|first5=Xavier|last6=Ventura|first6=Salvador|date=2007-02-27|title=AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides|url=https://doi.org/10.1186/1471-2105-8-65|journal=BMC Bioinformatics|volume=8|issue=1|pages=65|doi=10.1186/1471-2105-8-65|issn=1471-2105|pmc=1828741|pmid=17324296}}</ref>
|2007
|2007
|Web Servers -[http://thalis.biol.uoa.gr/AMYLPRED2/ AMLYPRED2] & [http://bioinf.uab.es/aggrescan/ AGGRESCAN]
|Web Servers -[http://thalis.biol.uoa.gr/AMYLPRED2/ AMLYPRED2] & [http://bioinf.uab.es/aggrescan/ AGGRESCAN]
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|Overall aggregation and amyloidogenic regions
|Overall aggregation and amyloidogenic regions
|-
|-
|'''[http://amypdb.genouest.org/e107_plugins/amypdb_aggregation/db_prediction_salsa.php Salsa]'''<ref>{{Cite journal|last=Zibaee|first=Shahin|last2=Makin|first2=O. Sumner|last3=Goedert|first3=Michel|last4=Serpell|first4=Louise C.|date=2007|title=A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone|url=https://onlinelibrary.wiley.com/doi/abs/10.1110/ps.062624507|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|issn=1469-896X|pmc=PMC2206631|pmid=17456743}}</ref>
|'''[http://amypdb.genouest.org/e107_plugins/amypdb_aggregation/db_prediction_salsa.php Salsa]'''<ref>{{Cite journal|last=Zibaee|first=Shahin|last2=Makin|first2=O. Sumner|last3=Goedert|first3=Michel|last4=Serpell|first4=Louise C.|date=2007|title=A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone|url=https://onlinelibrary.wiley.com/doi/abs/10.1110/ps.062624507|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|issn=1469-896X|pmc=2206631|pmid=17456743}}</ref>
|2007
|2007
|[http://amypdb.genouest.org/e107_plugins/amypdb_aggregation/db_prediction_salsa.php Web server] - AMYPdb<ref>{{Cite journal|last=Pawlicki|first=Sandrine|last2=Le Béchec|first2=Antony|last3=Delamarche|first3=Christian|date=2008-06-10|title=AMYPdb: A database dedicated to amyloid precursor proteins|url=https://doi.org/10.1186/1471-2105-9-273|journal=BMC Bioinformatics|volume=9|issue=1|pages=273|doi=10.1186/1471-2105-9-273|issn=1471-2105|pmc=PMC2442844|pmid=18544157}}</ref>
|[http://amypdb.genouest.org/e107_plugins/amypdb_aggregation/db_prediction_salsa.php Web server] - AMYPdb<ref>{{Cite journal|last=Pawlicki|first=Sandrine|last2=Le Béchec|first2=Antony|last3=Delamarche|first3=Christian|date=2008-06-10|title=AMYPdb: A database dedicated to amyloid precursor proteins|url=https://doi.org/10.1186/1471-2105-9-273|journal=BMC Bioinformatics|volume=9|issue=1|pages=273|doi=10.1186/1471-2105-9-273|issn=1471-2105|pmc=2442844|pmid=18544157}}</ref>
|'''Phenomenological'''
|'''Phenomenological'''
Prediction of the aggregation proposities of a single or multiple sequences.
Prediction of the aggregation proposities of a single or multiple sequences.
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''[http://www.mobioinfor.cn/pafig/ Pafig]'''<ref>{{Cite journal|last=Tian|first=Jian|last2=Wu|first2=Ningfeng|last3=Guo|first3=Jun|last4=Fan|first4=Yunliu|date=2009-01-30|title=Prediction of amyloid fibril-forming segments based on a support vector machine|url=https://doi.org/10.1186/1471-2105-10-S1-S45|journal=BMC Bioinformatics|volume=10|issue=1|pages=S45|doi=10.1186/1471-2105-10-S1-S45|issn=1471-2105|pmc=PMC2648769|pmid=19208147}}</ref>
|'''[http://www.mobioinfor.cn/pafig/ Pafig]'''<ref>{{Cite journal|last=Tian|first=Jian|last2=Wu|first2=Ningfeng|last3=Guo|first3=Jun|last4=Fan|first4=Yunliu|date=2009-01-30|title=Prediction of amyloid fibril-forming segments based on a support vector machine|url=https://doi.org/10.1186/1471-2105-10-S1-S45|journal=BMC Bioinformatics|volume=10|issue=1|pages=S45|doi=10.1186/1471-2105-10-S1-S45|issn=1471-2105|pmc=2648769|pmid=19208147}}</ref>
|2009
|2009
|Web server- [http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Web server- [http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''Net-CSSP<ref>{{Cite journal|last=Kim|first=C.|last2=Choi|first2=J.|last3=Lee|first3=S. J.|last4=Welsh|first4=W. J.|last5=Yoon|first5=S.|date=2009-07-01|title=NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation|url=https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp351|journal=Nucleic Acids Research|language=en|volume=37|issue=Web Server|pages=W469–W473|doi=10.1093/nar/gkp351|issn=0305-1048|pmc=PMC2703942|pmid=19468045}}</ref>'''<ref>{{Cite journal|last=Yoon|first=Sukjoon|last2=Welsh|first2=William J.|last3=Jung|first3=Heeyoung|last4=Yoo|first4=Young Do|date=2007-10|title=CSSP2: An improved method for predicting contact-dependent secondary structure propensity|url=https://linkinghub.elsevier.com/retrieve/pii/S1476927107000837|journal=Computational Biology and Chemistry|language=en|volume=31|issue=5-6|pages=373–377|doi=10.1016/j.compbiolchem.2007.06.002}}</ref><ref>{{Cite journal|last=Yoon|first=Sukjoon|last2=Welsh|first2=William J.|date=2005-04-22|title=Rapid assessment of contact-dependent secondary structure propensity: Relevance to amyloidogenic sequences|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.20477|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=60|issue=1|pages=110–117|doi=10.1002/prot.20477}}</ref><ref>{{Cite journal|last=Yoon|first=Sukjoon|last2=Welsh|first2=William J.|date=2004-08|title=Detecting hidden sequence propensity for amyloid fibril formation|url=http://dx.doi.org/10.1110/ps.04790604|journal=Protein Science|volume=13|issue=8|pages=2149–2160|doi=10.1110/ps.04790604|issn=0961-8368}}</ref>
|'''Net-CSSP<ref>{{Cite journal|last=Kim|first=C.|last2=Choi|first2=J.|last3=Lee|first3=S. J.|last4=Welsh|first4=W. J.|last5=Yoon|first5=S.|date=2009-07-01|title=NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation|url=https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp351|journal=Nucleic Acids Research|language=en|volume=37|issue=Web Server|pages=W469–W473|doi=10.1093/nar/gkp351|issn=0305-1048|pmc=2703942|pmid=19468045}}</ref>'''<ref>{{Cite journal|last=Yoon|first=Sukjoon|last2=Welsh|first2=William J.|last3=Jung|first3=Heeyoung|last4=Yoo|first4=Young Do|date=October 2007|title=CSSP2: An improved method for predicting contact-dependent secondary structure propensity|url=https://linkinghub.elsevier.com/retrieve/pii/S1476927107000837|journal=Computational Biology and Chemistry|language=en|volume=31|issue=5-6|pages=373–377|doi=10.1016/j.compbiolchem.2007.06.002}}</ref><ref>{{Cite journal|last=Yoon|first=Sukjoon|last2=Welsh|first2=William J.|date=2005-04-22|title=Rapid assessment of contact-dependent secondary structure propensity: Relevance to amyloidogenic sequences|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.20477|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=60|issue=1|pages=110–117|doi=10.1002/prot.20477}}</ref><ref>{{Cite journal|last=Yoon|first=Sukjoon|last2=Welsh|first2=William J.|date=August 2004|title=Detecting hidden sequence propensity for amyloid fibril formation|url=http://dx.doi.org/10.1110/ps.04790604|journal=Protein Science|volume=13|issue=8|pages=2149–2160|doi=10.1110/ps.04790604|issn=0961-8368}}</ref>
|2020
|2020
|Web Server - [http://cssp2.sookmyung.ac.kr/ Net-CSSP]
|Web Server - [http://cssp2.sookmyung.ac.kr/ Net-CSSP]
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|Amyloidogenic propensity regions
|Amyloidogenic propensity regions
|-
|-
|'''Betascan'''<ref>{{Cite journal|last=Jr|first=Allen W. Bryan|last2=Menke|first2=Matthew|last3=Cowen|first3=Lenore J.|last4=Lindquist|first4=Susan L.|last5=Berger|first5=Bonnie|date=2009-03-27|title=BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis|url=https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000333|journal=PLOS Computational Biology|language=en|volume=5|issue=3|pages=e1000333|doi=10.1371/journal.pcbi.1000333|issn=1553-7358|pmc=PMC2653728|pmid=19325876}}</ref>
|'''Betascan'''<ref>{{Cite journal|last=Jr|first=Allen W. Bryan|last2=Menke|first2=Matthew|last3=Cowen|first3=Lenore J.|last4=Lindquist|first4=Susan L.|last5=Berger|first5=Bonnie|date=2009-03-27|title=BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis|url=https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000333|journal=PLOS Computational Biology|language=en|volume=5|issue=3|pages=e1000333|doi=10.1371/journal.pcbi.1000333|issn=1553-7358|pmc=2653728|pmid=19325876}}</ref>
|2009
|2009
|Web Server - [http://cb.csail.mit.edu/cb/betascan/betascan.html Betascan]
|Web Server - [http://cb.csail.mit.edu/cb/betascan/betascan.html Betascan]
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''Waltz'''<ref>{{Cite journal|last=Oliveberg|first=Mikael|date=2010-03|title=Waltz, an exciting new move in amyloid prediction|url=http://www.nature.com/articles/nmeth0310-187|journal=Nature Methods|language=en|volume=7|issue=3|pages=187–188|doi=10.1038/nmeth0310-187|issn=1548-7091}}</ref><ref>{{Cite journal|last=Maurer-Stroh|first=Sebastian|last2=Debulpaep|first2=Maja|last3=Kuemmerer|first3=Nico|last4=de la Paz|first4=Manuela Lopez|last5=Martins|first5=Ivo Cristiano|last6=Reumers|first6=Joke|last7=Morris|first7=Kyle L.|last8=Copland|first8=Alastair|last9=Serpell|first9=Louise|last10=Serrano|first10=Luis|last11=Schymkowitz|first11=Joost W. H.|date=2010-03|title=Exploring the sequence determinants of amyloid structure using position-specific scoring matrices|url=https://www.nature.com/articles/nmeth.1432|journal=Nature Methods|language=en|volume=7|issue=3|pages=237–242|doi=10.1038/nmeth.1432|issn=1548-7105}}</ref>
|'''Waltz'''<ref>{{Cite journal|last=Oliveberg|first=Mikael|date=March 2010|title=Waltz, an exciting new move in amyloid prediction|url=http://www.nature.com/articles/nmeth0310-187|journal=Nature Methods|language=en|volume=7|issue=3|pages=187–188|doi=10.1038/nmeth0310-187|issn=1548-7091}}</ref><ref>{{Cite journal|last=Maurer-Stroh|first=Sebastian|last2=Debulpaep|first2=Maja|last3=Kuemmerer|first3=Nico|last4=de la Paz|first4=Manuela Lopez|last5=Martins|first5=Ivo Cristiano|last6=Reumers|first6=Joke|last7=Morris|first7=Kyle L.|last8=Copland|first8=Alastair|last9=Serpell|first9=Louise|last10=Serrano|first10=Luis|last11=Schymkowitz|first11=Joost W. H.|date=March 2010|title=Exploring the sequence determinants of amyloid structure using position-specific scoring matrices|url=https://www.nature.com/articles/nmeth.1432|journal=Nature Methods|language=en|volume=7|issue=3|pages=237–242|doi=10.1038/nmeth.1432|issn=1548-7105}}</ref>
|2010
|2010
|Web Server - [https://waltz.switchlab.org/ Waltz] &
|Web Server - [https://waltz.switchlab.org/ Waltz] &
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''STITCHER'''<ref>{{Cite journal|last=Bryan|first=Allen W.|last2=O'Donnell|first2=Charles W.|last3=Menke|first3=Matthew|last4=Cowen|first4=Lenore J.|last5=Lindquist|first5=Susan|last6=Berger|first6=Bonnie|date=2012-02|title=STITCHER: Dynamic assembly of likely amyloid and prion β‐structures from secondary structure predictions|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.23203|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=80|issue=2|pages=410–420|doi=10.1002/prot.23203|issn=0887-3585|pmc=PMC3298606|pmid=22095906}}</ref>
|'''STITCHER'''<ref>{{Cite journal|last=Bryan|first=Allen W.|last2=O'Donnell|first2=Charles W.|last3=Menke|first3=Matthew|last4=Cowen|first4=Lenore J.|last5=Lindquist|first5=Susan|last6=Berger|first6=Bonnie|date=February 2012|title=STITCHER: Dynamic assembly of likely amyloid and prion β‐structures from secondary structure predictions|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.23203|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=80|issue=2|pages=410–420|doi=10.1002/prot.23203|issn=0887-3585|pmc=3298606|pmid=22095906}}</ref>
|2012
|2012
| Web Server - [http://stitcher.csail.mit.edu Stitcher] (currently offline)
| Web Server - [http://stitcher.csail.mit.edu Stitcher] (currently offline)
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''MetAmyl'''<ref>{{Cite journal|last=Tian|first=Jian|last2=Wu|first2=Ningfeng|last3=Guo|first3=Jun|last4=Fan|first4=Yunliu|date=2009-01|title=Prediction of amyloid fibril-forming segments based on a support vector machine|url=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-S1-S45|journal=BMC Bioinformatics|language=en|volume=10|issue=S1|pages=S45|doi=10.1186/1471-2105-10-S1-S45|issn=1471-2105|pmc=PMC2648769|pmid=19208147}}</ref><ref>{{Cite journal|last=Zibaee|first=Shahin|last2=Makin|first2=O. Sumner|last3=Goedert|first3=Michel|last4=Serpell|first4=Louise C.|date=2007-05|title=A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone|url=http://doi.wiley.com/10.1110/ps.062624507|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|pmc=PMC2206631|pmid=17456743}}</ref><ref>{{Cite journal|last=Maurer-Stroh|first=Sebastian|last2=Debulpaep|first2=Maja|last3=Kuemmerer|first3=Nico|last4=de la Paz|first4=Manuela Lopez|last5=Martins|first5=Ivo Cristiano|last6=Reumers|first6=Joke|last7=Morris|first7=Kyle L|last8=Copland|first8=Alastair|last9=Serpell|first9=Louise|last10=Serrano|first10=Luis|last11=Schymkowitz|first11=Joost W H|date=2010-03|title=Exploring the sequence determinants of amyloid structure using position-specific scoring matrices|url=http://www.nature.com/articles/nmeth.1432|journal=Nature Methods|language=en|volume=7|issue=3|pages=237–242|doi=10.1038/nmeth.1432|issn=1548-7091}}</ref><ref>{{Cite journal|last=Garbuzynskiy|first=S. O.|last2=Lobanov|first2=M. Yu.|last3=Galzitskaya|first3=O. V.|date=2010-02-01|title=FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence|url=https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp691|journal=Bioinformatics|language=en|volume=26|issue=3|pages=326–332|doi=10.1093/bioinformatics/btp691|issn=1367-4803}}</ref>
|'''MetAmyl'''<ref>{{Cite journal|last=Tian|first=Jian|last2=Wu|first2=Ningfeng|last3=Guo|first3=Jun|last4=Fan|first4=Yunliu|date=January 2009|title=Prediction of amyloid fibril-forming segments based on a support vector machine|url=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-S1-S45|journal=BMC Bioinformatics|language=en|volume=10|issue=S1|pages=S45|doi=10.1186/1471-2105-10-S1-S45|issn=1471-2105|pmc=2648769|pmid=19208147}}</ref><ref>{{Cite journal|last=Zibaee|first=Shahin|last2=Makin|first2=O. Sumner|last3=Goedert|first3=Michel|last4=Serpell|first4=Louise C.|date=May 2007|title=A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone|url=http://doi.wiley.com/10.1110/ps.062624507|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|pmc=2206631|pmid=17456743}}</ref><ref>{{Cite journal|last=Maurer-Stroh|first=Sebastian|last2=Debulpaep|first2=Maja|last3=Kuemmerer|first3=Nico|last4=de la Paz|first4=Manuela Lopez|last5=Martins|first5=Ivo Cristiano|last6=Reumers|first6=Joke|last7=Morris|first7=Kyle L|last8=Copland|first8=Alastair|last9=Serpell|first9=Louise|last10=Serrano|first10=Luis|last11=Schymkowitz|first11=Joost W H|date=March 2010|title=Exploring the sequence determinants of amyloid structure using position-specific scoring matrices|url=http://www.nature.com/articles/nmeth.1432|journal=Nature Methods|language=en|volume=7|issue=3|pages=237–242|doi=10.1038/nmeth.1432|issn=1548-7091}}</ref><ref>{{Cite journal|last=Garbuzynskiy|first=S. O.|last2=Lobanov|first2=M. Yu.|last3=Galzitskaya|first3=O. V.|date=2010-02-01|title=FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence|url=https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp691|journal=Bioinformatics|language=en|volume=26|issue=3|pages=326–332|doi=10.1093/bioinformatics/btp691|issn=1367-4803}}</ref>
|2013
|2013
|Web Server - [http://metamyl.genouest.org/e107_plugins/metamyl_aggregation/db_prediction_meta.php MetAmyl]
|Web Server - [http://metamyl.genouest.org/e107_plugins/metamyl_aggregation/db_prediction_meta.php MetAmyl]
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|Overall generic and amyloidogenic regions based on the consensus
|Overall generic and amyloidogenic regions based on the consensus
|-
|-
|'''AmylPred2'''<ref>{{Cite journal|last=Tsolis|first=Antonios C.|last2=Papandreou|first2=Nikos C.|last3=Iconomidou|first3=Vassiliki A.|last4=Hamodrakas|first4=Stavros J.|date=2013-01-10|title=A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins|url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054175|journal=PLOS ONE|language=en|volume=8|issue=1|pages=e54175|doi=10.1371/journal.pone.0054175|issn=1932-6203|pmc=PMC3542318|pmid=23326595}}</ref>
|'''AmylPred2'''<ref>{{Cite journal|last=Tsolis|first=Antonios C.|last2=Papandreou|first2=Nikos C.|last3=Iconomidou|first3=Vassiliki A.|last4=Hamodrakas|first4=Stavros J.|date=2013-01-10|title=A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins|url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054175|journal=PLOS ONE|language=en|volume=8|issue=1|pages=e54175|doi=10.1371/journal.pone.0054175|issn=1932-6203|pmc=3542318|pmid=23326595}}</ref>
|2013
|2013
|Web Server - [http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Web Server - [http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
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|Overall generic and amyloidogenic regions based on the consensus
|Overall generic and amyloidogenic regions based on the consensus
|-
|-
|'''PASTA 2.0'''<ref>{{Cite journal|last=Walsh|first=Ian|last2=Seno|first2=Flavio|last3=Tosatto|first3=Silvio C.E.|last4=Trovato|first4=Antonio|date=2014-05-21|title=PASTA 2.0: an improved server for protein aggregation prediction|url=https://doi.org/10.1093/nar/gku399|journal=Nucleic Acids Research|volume=42|issue=W1|pages=W301–W307|doi=10.1093/nar/gku399|issn=1362-4962|pmc=PMC4086119|pmid=24848016}}</ref>
|'''PASTA 2.0'''<ref>{{Cite journal|last=Walsh|first=Ian|last2=Seno|first2=Flavio|last3=Tosatto|first3=Silvio C.E.|last4=Trovato|first4=Antonio|date=2014-05-21|title=PASTA 2.0: an improved server for protein aggregation prediction|url=https://doi.org/10.1093/nar/gku399|journal=Nucleic Acids Research|volume=42|issue=W1|pages=W301–W307|doi=10.1093/nar/gku399|issn=1362-4962|pmc=4086119|pmid=24848016}}</ref>
|2014
|2014
|Web Server - [http://old.protein.bio.unipd.it/pasta2/index.html PASTA 2.0]
|Web Server - [http://old.protein.bio.unipd.it/pasta2/index.html PASTA 2.0]
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|Amyloidogenic regions, energy, and beta-sheet orientation in aggregates
|Amyloidogenic regions, energy, and beta-sheet orientation in aggregates
|-
|-
|'''FISH Amyloid'''<ref>{{Cite journal|last=Gasior|first=Pawel|last2=Kotulska|first2=Malgorzata|date=2014-12|title=FISH Amyloid – a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids|url=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-54|journal=BMC Bioinformatics|language=en|volume=15|issue=1|pages=54|doi=10.1186/1471-2105-15-54|issn=1471-2105|pmc=PMC3941796|pmid=24564523}}</ref>
|'''FISH Amyloid'''<ref>{{Cite journal|last=Gasior|first=Pawel|last2=Kotulska|first2=Malgorzata|date=December 2014|title=FISH Amyloid – a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids|url=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-54|journal=BMC Bioinformatics|language=en|volume=15|issue=1|pages=54|doi=10.1186/1471-2105-15-54|issn=1471-2105|pmc=3941796|pmid=24564523}}</ref>
|2014
|2014
|Web Server - [http://comprec-lin.iiar.pwr.edu.pl/fishInput/ Comprec] (currently offline)
|Web Server - [http://comprec-lin.iiar.pwr.edu.pl/fishInput/ Comprec] (currently offline)
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''GAP'''<ref>{{Cite journal|last=Thangakani|first=A. Mary|last2=Kumar|first2=Sandeep|last3=Nagarajan|first3=R.|last4=Velmurugan|first4=D.|last5=Gromiha|first5=M. Michael|date=2014-03-28|title=GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies|url=https://doi.org/10.1093/bioinformatics/btu167|journal=Bioinformatics|volume=30|issue=14|pages=1983–1990|doi=10.1093/bioinformatics/btu167|issn=1460-2059}}</ref><ref>{{Cite journal|last=Thangakani|first=Anthony Mary|last2=Kumar|first2=Sandeep|last3=Velmurugan|first3=Devadasan|last4=Gromiha|first4=Maria Siluvay Michael|date=2012-04|title=How do thermophilic proteins resist aggregation?|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.24002|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=80|issue=4|pages=1003–1015|doi=10.1002/prot.24002}}</ref><ref>{{Citation|last=Gromiha|first=M. Michael|title=Sequence Analysis and Discrimination of Amyloid and Non-amyloid Peptides|date=2012|url=http://link.springer.com/10.1007/978-3-642-31837-5_65|work=Emerging Intelligent Computing Technology and Applications|volume=304|pages=447–452|editor-last=Huang|editor-first=De-Shuang|place=Berlin, Heidelberg|publisher=Springer Berlin Heidelberg|doi=10.1007/978-3-642-31837-5_65|isbn=978-3-642-31836-8|access-date=2021-11-26|last2=Thangakani|first2=A. Mary|last3=Kumar|first3=Sandeep|last4=Velmurugan|first4=D.|editor2-last=Gupta|editor2-first=Phalguni|editor3-last=Zhang|editor3-first=Xiang|editor4-last=Premaratne|editor4-first=Prashan}}</ref><ref>{{Cite journal|last=Thangakani|first=A Mary|last2=Kumar|first2=Sandeep|last3=Velmurugan|first3=D|last4=Gromiha|first4=M Michael|date=2013-05|title=Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences|url=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S8-S6|journal=BMC Bioinformatics|language=en|volume=14|issue=S8|pages=S6|doi=10.1186/1471-2105-14-S8-S6|issn=1471-2105|pmc=PMC3654898|pmid=23815227}}</ref><ref>{{Cite journal|last=Thangakani|first=A. Mary|last2=Kumar|first2=Sandeep|last3=Nagarajan|first3=R.|last4=Velmurugan|first4=D.|last5=Gromiha|first5=M. Michael|date=2014-03-28|title=GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies|url=https://doi.org/10.1093/bioinformatics/btu167|journal=Bioinformatics|volume=30|issue=14|pages=1983–1990|doi=10.1093/bioinformatics/btu167|issn=1460-2059}}</ref>
|'''GAP'''<ref>{{Cite journal|last=Thangakani|first=A. Mary|last2=Kumar|first2=Sandeep|last3=Nagarajan|first3=R.|last4=Velmurugan|first4=D.|last5=Gromiha|first5=M. Michael|date=2014-03-28|title=GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies|url=https://doi.org/10.1093/bioinformatics/btu167|journal=Bioinformatics|volume=30|issue=14|pages=1983–1990|doi=10.1093/bioinformatics/btu167|issn=1460-2059}}</ref><ref>{{Cite journal|last=Thangakani|first=Anthony Mary|last2=Kumar|first2=Sandeep|last3=Velmurugan|first3=Devadasan|last4=Gromiha|first4=Maria Siluvay Michael|date=April 2012|title=How do thermophilic proteins resist aggregation?|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.24002|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=80|issue=4|pages=1003–1015|doi=10.1002/prot.24002}}</ref><ref>{{Citation|last=Gromiha|first=M. Michael|title=Sequence Analysis and Discrimination of Amyloid and Non-amyloid Peptides|date=2012|url=http://link.springer.com/10.1007/978-3-642-31837-5_65|work=Emerging Intelligent Computing Technology and Applications|volume=304|pages=447–452|editor-last=Huang|editor-first=De-Shuang|place=Berlin, Heidelberg|publisher=Springer Berlin Heidelberg|doi=10.1007/978-3-642-31837-5_65|isbn=978-3-642-31836-8|access-date=2021-11-26|last2=Thangakani|first2=A. Mary|last3=Kumar|first3=Sandeep|last4=Velmurugan|first4=D.|editor2-last=Gupta|editor2-first=Phalguni|editor3-last=Zhang|editor3-first=Xiang|editor4-last=Premaratne|editor4-first=Prashan}}</ref><ref>{{Cite journal|last=Thangakani|first=A Mary|last2=Kumar|first2=Sandeep|last3=Velmurugan|first3=D|last4=Gromiha|first4=M Michael|date=May 2013|title=Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences|url=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S8-S6|journal=BMC Bioinformatics|language=en|volume=14|issue=S8|pages=S6|doi=10.1186/1471-2105-14-S8-S6|issn=1471-2105|pmc=3654898|pmid=23815227}}</ref><ref>{{Cite journal|last=Thangakani|first=A. Mary|last2=Kumar|first2=Sandeep|last3=Nagarajan|first3=R.|last4=Velmurugan|first4=D.|last5=Gromiha|first5=M. Michael|date=2014-03-28|title=GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies|url=https://doi.org/10.1093/bioinformatics/btu167|journal=Bioinformatics|volume=30|issue=14|pages=1983–1990|doi=10.1093/bioinformatics/btu167|issn=1460-2059}}</ref>
|2014
|2014
|Web Server - [https://www.iitm.ac.in/bioinfo/GAP/ GAP]
|Web Server - [https://www.iitm.ac.in/bioinfo/GAP/ GAP]
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|Overall aggregation and amyloidogenic regions
|Overall aggregation and amyloidogenic regions
|-
|-
|'''APPNN'''<ref>{{Cite journal|last=Família|first=Carlos|last2=Dennison|first2=Sarah R.|last3=Quintas|first3=Alexandre|last4=Phoenix|first4=David A.|date=2015-08-04|editor-last=Permyakov|editor-first=Eugene A.|title=Prediction of Peptide and Protein Propensity for Amyloid Formation|url=https://dx.plos.org/10.1371/journal.pone.0134679|journal=PLOS ONE|language=en|volume=10|issue=8|pages=e0134679|doi=10.1371/journal.pone.0134679|issn=1932-6203|pmc=PMC4524629|pmid=26241652}}</ref>
|'''APPNN'''<ref>{{Cite journal|last=Família|first=Carlos|last2=Dennison|first2=Sarah R.|last3=Quintas|first3=Alexandre|last4=Phoenix|first4=David A.|date=2015-08-04|editor-last=Permyakov|editor-first=Eugene A.|title=Prediction of Peptide and Protein Propensity for Amyloid Formation|url=https://dx.plos.org/10.1371/journal.pone.0134679|journal=PLOS ONE|language=en|volume=10|issue=8|pages=e0134679|doi=10.1371/journal.pone.0134679|issn=1932-6203|pmc=4524629|pmid=26241652}}</ref>
|2015
|2015
|Download - [https://CRAN.R-project.org/package=appnn CRAN]
|Download - [https://CRAN.R-project.org/package=appnn CRAN]
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''ArchCandy'''<ref>{{Cite journal|last=Ahmed|first=Abdullah B.|last2=Znassi|first2=Nadia|last3=Château|first3=Marie‐Thérèse|last4=Kajava|first4=Andrey V.|date=2015-06|title=A structure‐based approach to predict predisposition to amyloidosis|url=https://onlinelibrary.wiley.com/doi/10.1016/j.jalz.2014.06.007|journal=Alzheimer's & Dementia|language=en|volume=11|issue=6|pages=681–690|doi=10.1016/j.jalz.2014.06.007|issn=1552-5260}}</ref>
|'''ArchCandy'''<ref>{{Cite journal|last=Ahmed|first=Abdullah B.|last2=Znassi|first2=Nadia|last3=Château|first3=Marie‐Thérèse|last4=Kajava|first4=Andrey V.|date=June 2015|title=A structure‐based approach to predict predisposition to amyloidosis|url=https://onlinelibrary.wiley.com/doi/10.1016/j.jalz.2014.06.007|journal=Alzheimer's & Dementia|language=en|volume=11|issue=6|pages=681–690|doi=10.1016/j.jalz.2014.06.007|issn=1552-5260}}</ref>
|2015
|2015
|Download- [https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=7 BiSMM]
|Download- [https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=7 BiSMM]
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|Overall generic and amyloidogenic regions
|Overall generic and amyloidogenic regions
|-
|-
|'''CamSol Structurally Corrected'''<ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Aprile|first2=Francesco A.|last3=Vendruscolo|first3=Michele|date=2015-01|title=The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283614005312|journal=Journal of Molecular Biology|language=en|volume=427|issue=2|pages=478–490|doi=10.1016/j.jmb.2014.09.026}}</ref><ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Amery|first2=Leanne|last3=Ekizoglou|first3=Sofia|last4=Vendruscolo|first4=Michele|last5=Popovic|first5=Bojana|date=2017-12|title=Rapid and accurate in silico solubility screening of a monoclonal antibody library|url=http://www.nature.com/articles/s41598-017-07800-w|journal=Scientific Reports|language=en|volume=7|issue=1|pages=8200|doi=10.1038/s41598-017-07800-w|issn=2045-2322|pmc=PMC5558012|pmid=28811609}}</ref>
|'''CamSol Structurally Corrected'''<ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Aprile|first2=Francesco A.|last3=Vendruscolo|first3=Michele|date=January 2015|title=The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283614005312|journal=Journal of Molecular Biology|language=en|volume=427|issue=2|pages=478–490|doi=10.1016/j.jmb.2014.09.026}}</ref><ref>{{Cite journal|last=Sormanni|first=Pietro|last2=Amery|first2=Leanne|last3=Ekizoglou|first3=Sofia|last4=Vendruscolo|first4=Michele|last5=Popovic|first5=Bojana|date=December 2017|title=Rapid and accurate in silico solubility screening of a monoclonal antibody library|url=http://www.nature.com/articles/s41598-017-07800-w|journal=Scientific Reports|language=en|volume=7|issue=1|pages=8200|doi=10.1038/s41598-017-07800-w|issn=2045-2322|pmc=5558012|pmid=28811609}}</ref>
|2017
|2017
|Web Server - [https://www-cohsoftware.ch.cam.ac.uk/ Ch'''e'''mistry of Health]
|Web Server - [https://www-cohsoftware.ch.cam.ac.uk/ Ch'''e'''mistry of Health]
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|Exposed aggregation-prone patches and mutated variants design
|Exposed aggregation-prone patches and mutated variants design
|-
|-
|'''SolubiS'''<ref>{{Cite journal|last=Van Durme|first=Joost|last2=De Baets|first2=Greet|last3=Van Der Kant|first3=Rob|last4=Ramakers|first4=Meine|last5=Ganesan|first5=Ashok|last6=Wilkinson|first6=Hannah|last7=Gallardo|first7=Rodrigo|last8=Rousseau|first8=Frederic|last9=Schymkowitz|first9=Joost|date=2016-08|title=Solubis: a webserver to reduce protein aggregation through mutation|url=https://academic.oup.com/peds/article-lookup/doi/10.1093/protein/gzw019|journal=Protein Engineering Design and Selection|language=en|volume=29|issue=8|pages=285–289|doi=10.1093/protein/gzw019|issn=1741-0126}}</ref><ref>{{Cite journal|last=De Baets|first=Greet|last2=Van Durme|first2=Joost|last3=van der Kant|first3=Rob|last4=Schymkowitz|first4=Joost|last5=Rousseau|first5=Frederic|date=2015-08-01|title=Solubis: optimize your protein: Fig. 1.|url=https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv162|journal=Bioinformatics|language=en|volume=31|issue=15|pages=2580–2582|doi=10.1093/bioinformatics/btv162|issn=1367-4803}}</ref>
|'''SolubiS'''<ref>{{Cite journal|last=Van Durme|first=Joost|last2=De Baets|first2=Greet|last3=Van Der Kant|first3=Rob|last4=Ramakers|first4=Meine|last5=Ganesan|first5=Ashok|last6=Wilkinson|first6=Hannah|last7=Gallardo|first7=Rodrigo|last8=Rousseau|first8=Frederic|last9=Schymkowitz|first9=Joost|date=August 2016|title=Solubis: a webserver to reduce protein aggregation through mutation|url=https://academic.oup.com/peds/article-lookup/doi/10.1093/protein/gzw019|journal=Protein Engineering Design and Selection|language=en|volume=29|issue=8|pages=285–289|doi=10.1093/protein/gzw019|issn=1741-0126}}</ref><ref>{{Cite journal|last=De Baets|first=Greet|last2=Van Durme|first2=Joost|last3=van der Kant|first3=Rob|last4=Schymkowitz|first4=Joost|last5=Rousseau|first5=Frederic|date=2015-08-01|title=Solubis: optimize your protein: Fig. 1.|url=https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv162|journal=Bioinformatics|language=en|volume=31|issue=15|pages=2580–2582|doi=10.1093/bioinformatics/btv162|issn=1367-4803}}</ref>
|2016
|2016
|Web Server - [https://solubis.switchlab.org/node/add/solubis-job SolubiS]
|Web Server - [https://solubis.switchlab.org/node/add/solubis-job SolubiS]
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|Aggregation propensity and stability vs mutations
|Aggregation propensity and stability vs mutations
|-
|-
|'''AmyloGram'''<ref>{{Cite journal|last=Burdukiewicz|first=Michał|last2=Sobczyk|first2=Piotr|last3=Rödiger|first3=Stefan|last4=Duda-Madej|first4=Anna|last5=Mackiewicz|first5=Paweł|last6=Kotulska|first6=Małgorzata|date=2017-10-11|title=Amyloidogenic motifs revealed by n-gram analysis|url=https://www.nature.com/articles/s41598-017-13210-9|journal=Scientific Reports|language=en|volume=7|issue=1|pages=12961|doi=10.1038/s41598-017-13210-9|issn=2045-2322|pmc=PMC5636826|pmid=29021608}}</ref>
|'''AmyloGram'''<ref>{{Cite journal|last=Burdukiewicz|first=Michał|last2=Sobczyk|first2=Piotr|last3=Rödiger|first3=Stefan|last4=Duda-Madej|first4=Anna|last5=Mackiewicz|first5=Paweł|last6=Kotulska|first6=Małgorzata|date=2017-10-11|title=Amyloidogenic motifs revealed by n-gram analysis|url=https://www.nature.com/articles/s41598-017-13210-9|journal=Scientific Reports|language=en|volume=7|issue=1|pages=12961|doi=10.1038/s41598-017-13210-9|issn=2045-2322|pmc=5636826|pmid=29021608}}</ref>
|2017
|2017
|Web Server - [http://biongram.biotech.uni.wroc.pl/AmyloGram/ AmyloGram]
|Web Server - [http://biongram.biotech.uni.wroc.pl/AmyloGram/ AmyloGram]
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|Overall aggregation and amyloidogenic regions
|Overall aggregation and amyloidogenic regions
|-
|-
|'''AggScore'''<ref>{{Cite journal|last=Sankar|first=Kannan|last2=Krystek|first2=Stanley R.|last3=Carl|first3=Stephen M.|last4=Day|first4=Tyler|last5=Maier|first5=Johannes K. X.|date=2018-11|title=AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.25594|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=86|issue=11|pages=1147–1156|doi=10.1002/prot.25594}}</ref>
|'''AggScore'''<ref>{{Cite journal|last=Sankar|first=Kannan|last2=Krystek|first2=Stanley R.|last3=Carl|first3=Stephen M.|last4=Day|first4=Tyler|last5=Maier|first5=Johannes K. X.|date=November 2018|title=AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches|url=https://onlinelibrary.wiley.com/doi/10.1002/prot.25594|journal=Proteins: Structure, Function, and Bioinformatics|language=en|volume=86|issue=11|pages=1147–1156|doi=10.1002/prot.25594}}</ref>
|2018
|2018
|Download??
|Download??
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|Amyloidogenic regions
|Amyloidogenic regions
|-
|-
|'''AGGRESCAN 3D 2.0'''<ref>{{Cite journal|last=Kuriata|first=Aleksander|last2=Iglesias|first2=Valentin|last3=Pujols|first3=Jordi|last4=Kurcinski|first4=Mateusz|last5=Kmiecik|first5=Sebastian|last6=Ventura|first6=Salvador|date=2019-05-03|title=Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility|url=https://doi.org/10.1093/nar/gkz321|journal=Nucleic Acids Research|volume=47|issue=W1|pages=W300–W307|doi=10.1093/nar/gkz321|issn=0305-1048|pmc=PMC6602499|pmid=31049593}}</ref><ref>{{Cite journal|last=Kuriata|first=Aleksander|last2=Iglesias|first2=Valentin|last3=Kurcinski|first3=Mateusz|last4=Ventura|first4=Salvador|last5=Kmiecik|first5=Sebastian|date=2019-03-02|title=Aggrescan3D standalone package for structure-based prediction of protein aggregation properties|url=https://doi.org/10.1093/bioinformatics/btz143|journal=Bioinformatics|volume=35|issue=19|pages=3834–3835|doi=10.1093/bioinformatics/btz143|issn=1367-4803}}</ref><ref>{{Cite journal|last=Zambrano|first=Rafael|last2=Jamroz|first2=Michal|last3=Szczasiuk|first3=Agata|last4=Pujols|first4=Jordi|last5=Kmiecik|first5=Sebastian|last6=Ventura|first6=Salvador|date=2015-04-16|title=AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures|url=https://doi.org/10.1093/nar/gkv359|journal=Nucleic Acids Research|volume=43|issue=W1|pages=W306–W313|doi=10.1093/nar/gkv359|issn=0305-1048|pmc=PMC4489226|pmid=25883144}}</ref><ref>{{Cite journal|last=Gil-Garcia|first=Marcos|last2=Bañó-Polo|first2=Manuel|last3=Varejão|first3=Nathalia|last4=Jamroz|first4=Michal|last5=Kuriata|first5=Aleksander|last6=Díaz-Caballero|first6=Marta|last7=Lascorz|first7=Jara|last8=Morel|first8=Bertrand|last9=Navarro|first9=Susanna|last10=Reverter|first10=David|last11=Kmiecik|first11=Sebastian|date=2018-09-04|title=Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility|url=https://doi.org/10.1021/acs.molpharmaceut.8b00341|journal=Molecular Pharmaceutics|volume=15|issue=9|pages=3846–3859|doi=10.1021/acs.molpharmaceut.8b00341|issn=1543-8384}}</ref><ref>{{Cite journal|last=Pujols|first=Jordi|last2=Iglesias|first2=Valentín|last3=Santos|first3=Jaime|last4=Kuriata|first4=Aleksander|last5=Kmiecik|first5=Sebastian|last6=Ventura|first6=Salvador|date=2021-04-14|title=A3D 2.0 update for the prediction and optimization of protein solubility|url=http://biorxiv.org/lookup/doi/10.1101/2021.04.13.439600|language=en|doi=10.1101/2021.04.13.439600}}</ref>
|'''AGGRESCAN 3D 2.0'''<ref>{{Cite journal|last=Kuriata|first=Aleksander|last2=Iglesias|first2=Valentin|last3=Pujols|first3=Jordi|last4=Kurcinski|first4=Mateusz|last5=Kmiecik|first5=Sebastian|last6=Ventura|first6=Salvador|date=2019-05-03|title=Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility|url=https://doi.org/10.1093/nar/gkz321|journal=Nucleic Acids Research|volume=47|issue=W1|pages=W300–W307|doi=10.1093/nar/gkz321|issn=0305-1048|pmc=6602499|pmid=31049593}}</ref><ref>{{Cite journal|last=Kuriata|first=Aleksander|last2=Iglesias|first2=Valentin|last3=Kurcinski|first3=Mateusz|last4=Ventura|first4=Salvador|last5=Kmiecik|first5=Sebastian|date=2019-03-02|title=Aggrescan3D standalone package for structure-based prediction of protein aggregation properties|url=https://doi.org/10.1093/bioinformatics/btz143|journal=Bioinformatics|volume=35|issue=19|pages=3834–3835|doi=10.1093/bioinformatics/btz143|issn=1367-4803}}</ref><ref>{{Cite journal|last=Zambrano|first=Rafael|last2=Jamroz|first2=Michal|last3=Szczasiuk|first3=Agata|last4=Pujols|first4=Jordi|last5=Kmiecik|first5=Sebastian|last6=Ventura|first6=Salvador|date=2015-04-16|title=AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures|url=https://doi.org/10.1093/nar/gkv359|journal=Nucleic Acids Research|volume=43|issue=W1|pages=W306–W313|doi=10.1093/nar/gkv359|issn=0305-1048|pmc=4489226|pmid=25883144}}</ref><ref>{{Cite journal|last=Gil-Garcia|first=Marcos|last2=Bañó-Polo|first2=Manuel|last3=Varejão|first3=Nathalia|last4=Jamroz|first4=Michal|last5=Kuriata|first5=Aleksander|last6=Díaz-Caballero|first6=Marta|last7=Lascorz|first7=Jara|last8=Morel|first8=Bertrand|last9=Navarro|first9=Susanna|last10=Reverter|first10=David|last11=Kmiecik|first11=Sebastian|date=2018-09-04|title=Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility|url=https://doi.org/10.1021/acs.molpharmaceut.8b00341|journal=Molecular Pharmaceutics|volume=15|issue=9|pages=3846–3859|doi=10.1021/acs.molpharmaceut.8b00341|issn=1543-8384}}</ref><ref>{{Cite journal|last=Pujols|first=Jordi|last2=Iglesias|first2=Valentín|last3=Santos|first3=Jaime|last4=Kuriata|first4=Aleksander|last5=Kmiecik|first5=Sebastian|last6=Ventura|first6=Salvador|date=2021-04-14|title=A3D 2.0 update for the prediction and optimization of protein solubility|url=http://biorxiv.org/lookup/doi/10.1101/2021.04.13.439600|language=en|doi=10.1101/2021.04.13.439600}}</ref>
|2019
|2019
|Web Server - [http://biocomp.chem.uw.edu.pl/A3D2/ Aggrescan3D]
|Web Server - [http://biocomp.chem.uw.edu.pl/A3D2/ Aggrescan3D]
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|Dynamic exposed aggregation-prone patches and mutated variants design
|Dynamic exposed aggregation-prone patches and mutated variants design
|-
|-
|'''Budapest amyloid predictor'''<ref>{{Cite journal|last=Keresztes|first=László|last2=Szögi|first2=Evelin|last3=Varga|first3=Bálint|last4=Farkas|first4=Viktor|last5=Perczel|first5=András|last6=Grolmusz|first6=Vince|date=2021-04|title=The Budapest Amyloid Predictor and Its Applications|url=https://www.mdpi.com/2218-273X/11/4/500|journal=Biomolecules|language=en|volume=11|issue=4|pages=500|doi=10.3390/biom11040500|pmc=PMC8067080|pmid=33810341}}</ref>
|'''Budapest amyloid predictor'''<ref>{{Cite journal|last=Keresztes|first=László|last2=Szögi|first2=Evelin|last3=Varga|first3=Bálint|last4=Farkas|first4=Viktor|last5=Perczel|first5=András|last6=Grolmusz|first6=Vince|date=April 2021|title=The Budapest Amyloid Predictor and Its Applications|url=https://www.mdpi.com/2218-273X/11/4/500|journal=Biomolecules|language=en|volume=11|issue=4|pages=500|doi=10.3390/biom11040500|pmc=8067080|pmid=33810341}}</ref>
|2021
|2021
|Web Server - [https://pitgroup.org/bap/ Budapest amyloid predictor]
|Web Server - [https://pitgroup.org/bap/ Budapest amyloid predictor]
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|Amyloidgenecity of hexapeptide
|Amyloidgenecity of hexapeptide
|-
|-
|'''ANuPP'''<ref>{{Cite journal|last=Prabakaran|first=R.|last2=Rawat|first2=Puneet|last3=Kumar|first3=Sandeep|last4=Michael Gromiha|first4=M.|date=2021-05|title=ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283620306252|journal=Journal of Molecular Biology|language=en|volume=433|issue=11|pages=166707|doi=10.1016/j.jmb.2020.11.006}}</ref>
|'''ANuPP'''<ref>{{Cite journal|last=Prabakaran|first=R.|last2=Rawat|first2=Puneet|last3=Kumar|first3=Sandeep|last4=Michael Gromiha|first4=M.|date=May 2021|title=ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283620306252|journal=Journal of Molecular Biology|language=en|volume=433|issue=11|pages=166707|doi=10.1016/j.jmb.2020.11.006}}</ref>
|2021
|2021
|Web Server - [https://web.iitm.ac.in/bioinfo2/ANuPP/homeseq1/ ANuPP]
|Web Server - [https://web.iitm.ac.in/bioinfo2/ANuPP/homeseq1/ ANuPP]
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|}
|}


== See Also ==
== See also ==
[https://phasage.eu/tool-box/ PhasAGE toolbox]
[https://phasage.eu/tool-box/ PhasAGE toolbox]


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<references />
<references />
*
*

[[Category:Protein structure]]
[[Category:Protein structure]]
[[Category:Structural bioinformatics software]]
[[Category:Structural bioinformatics software]]

Revision as of 12:58, 6 December 2021

List of Protein aggregation predictors

Computational methods that use protein sequence and/ or protein structure to predict protein aggregation. The table below, shows the main features of software for prediction of protein aggregation

Table 1
Method Last Update Acess (Web server/downloadable) Principle Input Output
Sequence / 3D Structure Additional parameters
Amyloidogenic Patten[1] 2004 Web Server- AMYLPRED2 Structure-related

Amyloidogenic pattern

Submissions are scanned for the existence of this pattern {P}-{PKRHW}-[VLSCWFNQE]-[ILTYWFNE]-[FIY]-{PKRH} at identity level, with the use of a simple custom script.

sequence - Amyloidogenic regions
Tango [2][3][4] 2004 Web Server-TANGO Phenomenological

Based on physico-chemical principles of secondary structure formation extended by the assumption that the core regions of an aggregate are fully buried.

sequence pH/ionic strength Overall aggregation and amyloidoidogenic regions
Zipper DB [5][6][7][8] 2010 Web Server- Zipper DB Structure-related

Structure based prediction of fribrillation propoensities, using crystal strucutrue of the fibril forming peptide NNQQNY from the sup 35 prion protein of Saccharomyces cerevisiae.

sequence - Amyloidogenic regions and, energy and beta-sheet conformation
Average Packing Density[9] 2006 Web Server-AMYLPRED2 Structure-related

Relates average packing density of residues to the formation of amyloid fibrils.

sequence - Amyloidogenic regions
Beta-strand contiguity[10] 2007 Web Server- AMYLPRED2 Phenomenological

Prediction of B-strand propensity score to locate in the amyloid fibril.

sequence - beta-strand formation
Hexapeptide Conformational Energy /Pre-amyl[11] 2007 Web Server- AMYLPRED2 Structure-related

Hexapeptides of a submitted protein are threaded onto over 2500 templates of microcrystallic structure of NNQQNY, energy values below -27.00 are considered as hits.

sequence - Amyloidogenic regions and energy
CamSol intrinsic[12][13] 2017 Web Server- Chemistry of Health Phenomenological

Sequence-based method of predicting protein solubility and generic aggregation propensity.

sequence pH Calculation of the overall intrinsic solubility score and solubility profile
AGGRESCAN[14] 2007 Web Servers -AMLYPRED2 & AGGRESCAN Phenomenological

Prediction of 'aggregation-prone' in protein sequences, based on an aggregation propensity scale for natural amino acids derived from in vivo experiments.

sequence - Overall aggregation and amyloidogenic regions
Salsa[15] 2007 Web server - AMYPdb[16] Phenomenological

Prediction of the aggregation proposities of a single or multiple sequences.

sequence hot spot lenght Amyloidogenic regions
Pafig[17] 2009 Web server- AMYLPRED2

Download

Phenomenological

Identification of Hexapeptides associated to amyloid fibrillar aggregates.

sequence - Amyloidogenic regions
Net-CSSP[18][19][20][21] 2020 Web Server - Net-CSSP

AMYLPRED2

Structure-related

Quantification of the influence of the tertiary interation on seconday structural preference.

sequence/pdb single/dual network-treshold Amyloidogenic propensity regions
Betascan[22] 2009 Web Server - Betascan

Download - Betascan

Structure-related

Predict the probability that particular portions of a protein will form amyloid.

sequence length Amyloidogenic regions
FoldAmyloid[23] 2010 Web Server - FoldAmyloid Structure-related

Prediction of amyloid regions using expected probability of hydrogen bonds formation and packing densitites of residues.

sequence scale, treshold, averaging frame Amyloidogenic regions
Waltz[24][25] 2010 Web Server - Waltz &

AMYLPRED2

Structure-related sequence pH, specificity, sensitivity Amyloidogenic regions
STITCHER[26] 2012 Web Server - Stitcher (currently offline) Structure-related sequence - Amyloidogenic regions
MetAmyl[27][28][29][30] 2013 Web Server - MetAmyl Consensus method sequence treshold Overall generic and amyloidogenic regions based on the consensus
AmylPred2[31] 2013 Web Server - AMYLPRED2 Consensus method sequence - Overall generic and amyloidogenic regions based on the consensus
PASTA 2.0[32] 2014 Web Server - PASTA 2.0 Structure-related

Predicts the most aggregation-prone portions and the corresponding β-strand inter-molecular pairing for multiple input sequences.

sequence top pairings and energies, mutations and protein-protein Amyloidogenic regions, energy, and beta-sheet orientation in aggregates
FISH Amyloid[33] 2014 Web Server - Comprec (currently offline) Structure-related sequence treshold Amyloidogenic regions
GAP[34][35][36][37][38] 2014 Web Server - GAP Structure-related

Identification of amyloid forming peptides and amorphous peptides using a dataset of 139 amyloids and 168 amorphous peptides.

sequence - Overall aggregation and amyloidogenic regions
APPNN[39] 2015 Download - CRAN Phenomenological

Amyloidogenicity propensity predictor based on a machine learning approach through recursive feature selection and feed-forward neural networks, taking advantage of newly published sequences with experimental, in vitro, evidence of amyloid formation.

sequence - Amyloidogenic regions
ArchCandy[40] 2015 Download- BiSMM Structure-related

Based on an assumption that protein sequences that are able to form β-arcades are amyloidogenic.

sequence - Amyloidogenic regions
Amyload[41] 2015 Web Server - Comprec (currently offline) Consensus method sequence - Overall generic and amyloidogenic regions
CamSol Structurally Corrected[42][43] 2017 Web Server - Chemistry of Health 3D structure pdb file pH, patch radius Exposed aggregation-prone patches and mutated variants design
SolubiS[44][45] 2016 Web Server - SolubiS 3D structure pdb file chain, treshold, gatekeeper Aggregation propensity and stability vs mutations
AmyloGram[46] 2017 Web Server - AmyloGram Phenomenological

AmyloGram predicts amyloid proteins using n-gram encoding and random forests.

sequence - Overall aggregation and amyloidogenic regions
AggScore[47] 2018 Download?? Structure-related

Method that uses the distribution of hydrophobic and electrostatic patches on the surface of the protein, factoring in the intensity and relative orientation of the respective surface patches into an aggregation propensity function that has been trained on a benchmark set of 31 adnectin proteins.

sequence - Amyloidogenic regions
AGGRESCAN 3D 2.0[48][49][50][51][52] 2019 Web Server - Aggrescan3D 3D structure pdb file dynamic mode, mutations, patch radius, stability, enhance solubility Dynamic exposed aggregation-prone patches and mutated variants design
Budapest amyloid predictor[53] 2021 Web Server - Budapest amyloid predictor Hexapeptide sequence Amyloidgenecity of hexapeptide
ANuPP[54] 2021 Web Server - ANuPP Hexapeptide and Sequence

Identification amyloid-fibril forming peptides and regions in protein sequences

sequence Amyloidogenic hexapeptides and aggregation prone regions
AggreRATE-Pred[55] 2018 Web Server - AggreRAE-Pred Structure-related

Predict changes in aggregation rate upon point mutations

sequence pdb mutations

See also

PhasAGE toolbox

Amyloid

Protein aggregation

References

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