| class="wikitable"
|+Table 1
! rowspan="2" |Method
! rowspan="2" |Last Update
! rowspan="2" |Access (Web server/downloadable)
! rowspan="2" |Principle
! colspan="2" |Input
! rowspan="2" |Output |
| Sequence / 3D Structure
!Additional parameters |
|---|
Amyloidogenic Patten[{{Cite journal|last1=Paz|first1=Manuela López de la|last2=Serrano|first2=Luis|date=2004-01-06|title=Sequence determinants of amyloid fibril formation|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|bibcode=2004PNAS..101...87L|doi-access=free}}]
|2004
|Web Server- [http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Secondary 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 [{{Cite journal|last1=Rousseau|first1=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|pmid=16434184|url-access=subscription}}][{{Cite journal|last1=Fernandez-Escamilla|first1=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|pmid=15361882|s2cid=41481025|issn=1087-0156|url-access=subscription}}][{{Cite journal|last1=Linding|first1=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|pmid=15313629|url-access=subscription}}]
|2004
|Web Server-[http://tango.crg.es/ 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 |
Average Packing Density[{{Cite journal|last1=Galzitskaya|first1=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|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|bibcode=2006PLSCB...2..177G |doi-access=free }}]
|2006
|Web Server-[http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Secondary structure-related
Relates average packing density of residues to the formation of amyloid fibrils.
|sequence
| -
|Amyloidogenic regions |
Beta-strand contiguity[{{Cite journal|last1=Zibaee|first1=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|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|pmc=2206631|pmid=17456743}}]
|2007
|Web Server- [http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Phenomenological
Prediction of B-strand propensity score to locate in the amyloid fibril.
|sequence
| -
|beta-strand formation |
Hexapeptide Conformational Energy /Pre-amyl[{{Cite journal|last1=Zhang|first1=Zhuqing|last2=Chen|first2=Hao|last3=Lai|first3=Luhua|date=2007-09-01|title=Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential|journal=Bioinformatics|volume=23|issue=17|pages=2218–2225|doi=10.1093/bioinformatics/btm325|pmid=17599928|issn=1367-4803|doi-access=free}}]
|2007
|Web Server- [http://aias.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Secondary 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 |
AGGRESCAN[{{Cite journal|last1=Conchillo-Solé|first1=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|journal=BMC Bioinformatics|volume=8|issue=1|pages=65|doi=10.1186/1471-2105-8-65|issn=1471-2105|pmc=1828741|pmid=17324296 |doi-access=free }}]
|2007
|Web Servers -[http://thalis.biol.uoa.gr/AMYLPRED2/ AMLYPRED2] & [http://bioinf.uab.es/aggrescan/ 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 |
[http://amypdb.genouest.org/e107_plugins/amypdb_aggregation/db_prediction_salsa.php Salsa][{{Cite journal|last1=Zibaee|first1=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|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|issn=1469-896X|pmc=2206631|pmid=17456743}}]
|2007
|[http://amypdb.genouest.org/e107_plugins/amypdb_aggregation/db_prediction_salsa.php Web server] - AMYPdb[{{Cite journal|last1=Pawlicki|first1=Sandrine|last2=Le Béchec|first2=Antony|last3=Delamarche|first3=Christian|date=2008-06-10|title=AMYPdb: A database dedicated to amyloid precursor proteins|journal=BMC Bioinformatics|volume=9|issue=1|pages=273|doi=10.1186/1471-2105-9-273|issn=1471-2105|pmc=2442844|pmid=18544157 |doi-access=free }}]
|Phenomenological
Prediction of the aggregation propensities single or multiple sequences based on physicochemical properties.
|sequence
|hot spot length
|Amyloidogenic regions |
[http://www.mobioinfor.cn/pafig/ Pafig][{{Cite journal|last1=Tian|first1=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|journal=BMC Bioinformatics|volume=10|issue=1|pages=S45|doi=10.1186/1471-2105-10-S1-S45|issn=1471-2105|pmc=2648769|pmid=19208147 |doi-access=free }}]
|2009
|Web server- [http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
[http://www.mobioinfor.cn/pafig/download.htm Download]
|Phenomenological
Identification of Hexapeptides associated to amyloid fibrillar aggregates.
|sequence
| -
|Amyloidogenic regions |
Net-CSSP[{{Cite journal|last1=Kim|first1=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|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}}][{{Cite journal|last1=Yoon|first1=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|pmid=17644485|url-access=subscription}}][{{Cite journal|last1=Yoon|first1=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|pmid=15849755|s2cid=44309651|url-access=subscription}}][{{Cite journal|last1=Yoon|first1=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|pmc=2279810| doi=10.1110/ps.04790604|pmid=15273309|issn=0961-8368}}]
|2020
|Web Server - [http://cssp2.sookmyung.ac.kr/ Net-CSSP]
[http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Secondary structure-related
Quantification of the influence of the tertiary interation on secondary structural preference.
|sequence/pdb
|single/dual network-threshold
|Amyloidogenic propensity regions |
Betascan[{{Cite journal|last1=Bryan|first1=Allen W. Jr.|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|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|bibcode=2009PLSCB...5E0333B |doi-access=free }}]
|2009
|Web Server - [http://cb.csail.mit.edu/cb/betascan/betascan.html Betascan]
Download - [http://cb.csail.mit.edu/cb/betascan/ Betascan]
|Secondary structure-related
Predict the probability that particular portions of a protein will form amyloid.
|sequence
|length
|Amyloidogenic regions |
FoldAmyloid[{{Cite journal|last1=Garbuzynskiy|first1=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|pmid=20019059|issn=1367-4803|url-access=subscription}}]
|2010
|Web Server - [http://bioinfo.protres.ru/fold-amyloid/ FoldAmyloid]
|Secondary structure-related
Prediction of amyloid regions using expected probability of hydrogen bonds formation and packing densitites of residues.
|sequence
|scale, threshold, averaging frame
|Amyloidogenic regions |
Waltz[{{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|pmid=20195250|s2cid=205417298|issn=1548-7091|url-access=subscription}}][{{Cite journal|last1=Maurer-Stroh|first1=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|pmid=20154676|s2cid=52874481|issn=1548-7105|url-access=subscription}}]
|2010
|Web Server - [https://waltz.switchlab.org/ Waltz] &
[http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Secondary structure-related
Application of position-specific substitution matrices (PSSM) obtained from amyloidogenic peptides.
|sequence
|pH, specificity, sensitivity
|Amyloidogenic regions |
Zipper DB [{{Cite journal|last1=Thompson|first1=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|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|bibcode=2006PNAS..103.4074T|doi-access=free}}][{{Cite journal|last1=Nelson|first1=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|journal=Nature|language=en|volume=435|issue=7043|pages=773–778|doi=10.1038/nature03680|issn=1476-4687|pmc=1479801|pmid=15944695|bibcode=2005Natur.435..773N}}][{{Cite journal|last1=Kuhlman|first1=Brian|last2=Baker|first2=David|date=2000-09-12|title=Native protein sequences are close to optimal for their structures|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|bibcode=2000PNAS...9710383K|doi-access=free}}][{{Cite journal|last1=Sawaya|first1=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|pmid=17468747|bibcode=2007Natur.447..453S|s2cid=4400866|issn=0028-0836|url-access=subscription}}]
|2010
|Web Server- [http://services.mbi.ucla.edu/zipperdb/submit Zipper DB]
|Secondary 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 |
STITCHER[{{Cite journal|last1=Bryan|first1=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|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}}]
|2012
| Web Server - [http://stitcher.csail.mit.edu Stitcher] (currently offline)
|Secondary structure-related
|sequence
| -
|Amyloidogenic regions |
MetAmyl[{{Cite journal|last1=Tian|first1=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|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 |doi-access=free }}][{{Cite journal|last1=Zibaee|first1=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|journal=Protein Science|language=en|volume=16|issue=5|pages=906–918|doi=10.1110/ps.062624507|pmc=2206631|pmid=17456743}}][{{Cite journal|last1=Maurer-Stroh|first1=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|pmid=20154676|s2cid=52874481|issn=1548-7091|url-access=subscription}}][{{Cite journal|last1=Garbuzynskiy|first1=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|pmid=20019059|issn=1367-4803|url-access=subscription}}]
|2013
|Web Server - [http://metamyl.genouest.org/e107_plugins/metamyl_aggregation/db_prediction_meta.php MetAmyl]
|Consensus method
Amyloidogenic patterns, average packing density, beta-strand contiguity, pafig, Net-CSSP, STITCHER
|sequence
|threshold
|Overall generic and amyloidogenic regions based on the consensus |
AmylPred2[{{Cite journal|last1=Tsolis|first1=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|journal=PLOS ONE|language=en|volume=8|issue=1|pages=e54175|doi=10.1371/journal.pone.0054175|issn=1932-6203|pmc=3542318|pmid=23326595|bibcode=2013PLoSO...854175T|doi-access=free}}]
|2013
|Web Server - [http://thalis.biol.uoa.gr/AMYLPRED2/ AMYLPRED2]
|Consensus method
Amyloidogenic patterns, average packing density, beta-strand contiguity, pafig, Net-CSSP, STITCHER
|sequence
| -
|Overall generic and amyloidogenic regions based on the consensus |
PASTA 2.0[{{Cite journal|last1=Walsh|first1=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}}]
|2014
|Web Server - [http://old.protein.bio.unipd.it/pasta2/index.html PASTA 2.0]
|Secondary 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[{{Cite journal|last1=Gasior|first1=Pawel|last2=Kotulska|first2=Malgorzata|date=December 2014|title=FISH Amyloid – a new method for finding amyloidogenic segments in proteins based on site specific {{sic|co-occu|rence|nolink=y}} of aminoacids|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 |doi-access=free }}]
|2014
|Web Server - [http://comprec-lin.iiar.pwr.edu.pl/fishInput/ Comprec] (currently offline)
|Secondary structure-related
|sequence
|threshold
|Amyloidogenic regions |
GAP[{{Cite journal|last1=Thangakani|first1=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|journal=Bioinformatics|volume=30|issue=14|pages=1983–1990|doi=10.1093/bioinformatics/btu167|pmid=24681906|issn=1460-2059|doi-access=free}}][{{Cite journal|last1=Thangakani|first1=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|pmid=22389104|s2cid=21496810|url-access=subscription}}][{{Citation|last1=Gromiha|first1=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.|series=Communications in Computer and Information Science |editor2-last=Gupta|editor2-first=Phalguni|editor3-last=Zhang|editor3-first=Xiang|editor4-last=Premaratne|editor4-first=Prashan|url-access=subscription}}][{{Cite journal|last1=Thangakani|first1=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|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 |doi-access=free }}]
|2014
|Web Server - [https://www.iitm.ac.in/bioinfo/GAP/ GAP]
|Secondary 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[{{Cite journal|last1=Família|first1=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|journal=PLOS ONE|language=en|volume=10|issue=8|pages=e0134679|doi=10.1371/journal.pone.0134679|issn=1932-6203|pmc=4524629|pmid=26241652|bibcode=2015PLoSO..1034679F|doi-access=free}}]
|2015
|Download - [https://CRAN.R-project.org/package=appnn 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[{{Cite journal|last1=Ahmed|first1=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|pmid=25150734|s2cid=3130411|issn=1552-5260|url-access=subscription}}]
|2015
|Download- [https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=7 BiSMM]
|Secondary structure-related
Based on an assumption that protein sequences that are able to form β-arcades are amyloidogenic.
|sequence
| -
|Amyloidogenic regions |
Amyload[{{Cite journal|last1=Wozniak|first1=Pawel P.|last2=Kotulska|first2=Malgorzata|date=2015-06-17|title=AmyLoad: website dedicated to amyloidogenic protein fragments|journal=Bioinformatics|volume=31|issue=20|pages=3395–3397|doi=10.1093/bioinformatics/btv375|pmid=26088800|issn=1367-4803|doi-access=free}}]
|2015
|Web Server - [http://comprec-lin.iiar.pwr.edu.pl/amyload/analysisPage/ Comprec] (currently offline)
|Consensus method
|sequence
| -
|Overall generic and amyloidogenic regions |
SolubiS[{{Cite journal|last1=Van Durme|first1=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|pmid=27284085|issn=1741-0126|doi-access=free|url-access=subscription}}][{{Cite journal|last1=De Baets|first1=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.|journal=Bioinformatics|language=en|volume=31|issue=15|pages=2580–2582|doi=10.1093/bioinformatics/btv162|pmid=25792555|issn=1367-4803|doi-access=free}}]
|2016
|Web Server - [https://solubis.switchlab.org/node/add/solubis-job SolubiS]
|3D structure
|pdb file
|chain, threshold, gatekeeper
|Aggregation propensity and stability vs mutations |
CamSol Structurally Corrected[{{Cite journal|last1=Sormanni|first1=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|pmid=25451785|url-access=subscription}}][{{Cite journal|last1=Sormanni|first1=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|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|bibcode=2017NatSR...7.8200S}}]
|2017
|Web Server - [https://www-cohsoftware.ch.cam.ac.uk/ Chemistry of Health]
|3D structure
|pdb file
|pH, patch radius
|Exposed aggregation-prone patches and mutated variants design |
CamSol intrinsic[{{Cite journal|last1=Sormanni|first1=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|pmid=25451785|url-access=subscription}}][{{Cite journal|last1=Sormanni|first1=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|journal=Scientific Reports|language=en|volume=7|issue=1|pages=8200|doi=10.1038/s41598-017-07800-w|pmid=28811609|pmc=5558012|bibcode=2017NatSR...7.8200S|issn=2045-2322}}]
|2017
|Web Server- [https://www-cohsoftware.ch.cam.ac.uk/ 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 |
AmyloGram[{{Cite journal|last1=Burdukiewicz|first1=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|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|bibcode=2017NatSR...712961B}}]
|2017
|Web Server - [http://biongram.biotech.uni.wroc.pl/AmyloGram/ AmyloGram]
|Phenomenological
AmyloGram predicts amyloid proteins using n-gram encoding and random forests.
|sequence
| -
|Overall aggregation and amyloidogenic regions |
BetaSerpentine[{{Cite journal|last1=Bondarev|first1=Stanislav A|last2=Bondareva|first2=Olga V|last3=Zhouravleva|first3=Galina A|last4=Kajava|first4=Andrey V|date=2017-10-04|title=BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures|journal=Bioinformatics|volume=34|issue=4|pages=599–608|doi=10.1093/bioinformatics/btx629|pmid=29444233|issn=1367-4803|doi-access=free}}]
|2017
|Web Server - [https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=25 BetaSerpentine-1.0]
|Sequence-related
Reconstruction of amyloid structures containing adjacent β-arches.
|sequence
| -
|Amyloidogenic regions |
AggScore[{{Cite journal|last1=Sankar|first1=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|pmid=30168197|s2cid=52131048|url-access=subscription}}]
|2018
|AggScore is available through [https://www.schrodinger.com/science-articles/aggregation-prediction-protein-surface-analyzer Schrödinger's BioLuminate Suite as of software release 2018-1.]
|Secondary 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 |
AggreRATE-Pred[{{Cite journal|last1=Rawat|first1=Puneet|last2=Prabakaran|first2=R|last3=Kumar|first3=Sandeep|last4=Gromiha|first4=M Michael|date=2019-10-10|title=AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation|url=https://doi.org/10.1093/bioinformatics/btz764|journal=Bioinformatics|volume=36|issue=5|pages=1439–1444|doi=10.1093/bioinformatics/btz764|pmid=31599925|issn=1367-4803|url-access=subscription}}]
|2018
|Web Server - [https://www.iitm.ac.in/bioinfo/aggrerate-pred/# AggreRAE-Pred]
|Secondary structure-related
Predict changes in aggregation rate upon point mutations
|sequence pdb
|mutations
| |
AGGRESCAN 3D 2.0[{{Cite journal|last1=Kuriata|first1=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}}][{{Cite journal|last1=Kuriata|first1=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|pmid=30825368|issn=1367-4803|url-access=subscription}}][{{Cite journal|last1=Zambrano|first1=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}}][{{Cite journal|last1=Gil-Garcia|first1=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|pmid=30036481|s2cid=206688348|issn=1543-8384|url-access=subscription}}][{{Cite journal|last1=Pujols|first1=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|s2cid=233329012|doi-access=free}}]
|2019
|Web Server - [http://biocomp.chem.uw.edu.pl/A3D2/ 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[{{Cite journal|last1=Keresztes|first1=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|journal=Biomolecules|language=en|volume=11|issue=4|pages=500|doi=10.3390/biom11040500|pmc=8067080|pmid=33810341|doi-access=free}}]
|2021
|Web Server - [https://pitgroup.org/bap/ Budapest amyloid predictor]
|Hexapeptide
|sequence
|
|Amyloidgenecity of hexapeptide |
ANuPP[{{Cite journal|last1=Prabakaran|first1=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|pmid=33972019|s2cid=228867153|url-access=subscription}}]
|2021
|Web Server - [https://web.iitm.ac.in/bioinfo2/ANuPP/homeseq1/ ANuPP]
|Hexapeptide and Sequence
Identification amyloid-fibril forming peptides and regions in protein sequences
|sequence
|
|Amyloidogenic hexapeptides and aggregation prone regions |