Protein aggregation predictors

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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.


Name	Last Update	Acess (Web server/downloadable)	Principle	Input		Output
Name	Last Update	Acess (Web server/downloadable)	Principle	Sequence / 3D Structure	Additional parameters	Output
AMYLPRED2 Amyloidogenic Patten^[1]	2004	Web Server	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	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	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
AMYLPRED2 Average Packing Density^[9]	2006	Web Server	Structure-related Relates average packing density of residues to the formation of amyloid fibrils.	sequence	-	Amyloidogenic regions
AMYLPRED2 Beta-strand contiguity^[10]	2007	Web Server	Phenomenological Prediction of B-strand propensity score to locate in the amyloid fibril.	sequence	-	beta-strand formation
Hexapeptide Conformational Energy /Pre-amyl	2007	AmylPred	Structure-related	sequence	-	Amyloidogenic regions and energy
CamSol intrinsic (Zyggregator)	2017	web server	Phenomenological	sequence	pH	Calculation of the overall intrinsic solubility score and solubility profile
AGGRESCAN	2007	web server/AmylPred	Phenomenological	sequence	-	Overall aggregation and amyloidogenic regions
SALSA	2007	Metamyl	Phenomenological	sequence	hot spot lenght	Amyloidogenic regions
Pafig	2009	downloable/AmylPred/Metamyl	Phenomenological	sequence	-	Amyloidogenic regions
Net-CSSP	2009	web server/AmylPred	Structure-related	sequence/pdb	single/dual network-treshold	Amyloidogenic propensity regions
PAGE	2009	-	Structure-related	sequence	-	Generic or beta-aggregation prone regions
Betascan	2009	web server/downloadable	Structure-related	sequence	length	Amyloidogenic regions
SAP	2009	-	3D structure	pdb file	-	Dynamic exposed hydrophobic pathces
FoldAmyloid	2010	web server/Metamyl	Structure-related	sequence	scale, treshold, averaging frame	Amyloidogenic regions
Waltz	2010	web server/AmylPred/Metamyl	Structure-related	sequence	pH, specificity, sensitivity	Amyloidogenic regions
STITCHER	2012	-	Structure-related	sequence	-	Amyloidogenic regions
MetAmyl	2013	web server	Consensus method	sequence	treshold	Overall generic and amyloidogenic regions based on the consensus
AmylPred2	2013	web server	Consensus method	sequence	-	Overall generic and amyloidogenic regions based on the consensus
PASTA 2.0	2014	web server/downloadable	Structure-related	sequence	top pairings and energies, mutations and protein-protein	Amyloidogenic regions, energy, and beta-sheet orientation in aggregates
FISH Amyloid	2014	web server/downloadable	Structure-related	sequence	treshold	Amyloidogenic regions
GAP	2014	web server	Structure-related	sequence	-	Overall aggregation and amyloidogenic regions
APPNN	2015	downloable	Phenomenological	sequence	-	Amyloidogenic regions
ArchCandy	2015	downloable	Structure-related	sequence	-	Amyloidogenic regions
Amyload	2015	web server	Consensus method	sequence	-	Overall generic and amyloidogenic regions
CamSol Structurally Corrected	2015	webserver	3D structure	pdb file	pH, patch radius	Exposed aggregation-prone patches and mutated variants design
Solubis	2016	web server	3D structure	pdb file	chain, treshold, gatekeeper	Aggregation propensity and stability vs mutations
AmyloGram	2017	web server	Phenomenological	sequence	-	Overall aggregation and amyloidogenic regions
AggScore	2018	downloable	Structure-related	sequence	-	Amyloidogenic regions
AGGRESCAN 3D 2.0	2019	web server	3D structure	pdb file	dynamic mode, mutations, patch radius, stability, enhance solubility	Dynamic exposed aggregation-prone patches and mutated variants design

References

^ Paz, Manuela López de la; Serrano, Luis (2004-01-06). "Sequence determinants of amyloid fibril formation". Proceedings of the National Academy of Sciences. 101 (1): 87–92. doi:10.1073/pnas.2634884100. ISSN 0027-8424. PMC 314143. PMID 14691246.{{cite journal}}: CS1 maint: PMC format (link)
^ Rousseau, F; Schymkowitz, J; Serrano, L (2006-02). "Protein aggregation and amyloidosis: confusion of the kinds?". Current Opinion in Structural Biology. 16 (1): 118–126. doi:10.1016/j.sbi.2006.01.011. {{cite journal}}: Check date values in: |date= (help)
^ Fernandez-Escamilla, Ana-Maria; Rousseau, Frederic; Schymkowitz, Joost; Serrano, Luis (2004-10). "Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins". Nature Biotechnology. 22 (10): 1302–1306. doi:10.1038/nbt1012. ISSN 1087-0156. {{cite journal}}: Check date values in: |date= (help)
^ Linding, Rune; Schymkowitz, Joost; Rousseau, Frederic; Diella, Francesca; Serrano, Luis (2004-09). "A Comparative Study of the Relationship Between Protein Structure and β-Aggregation in Globular and Intrinsically Disordered Proteins". Journal of Molecular Biology. 342 (1): 345–353. doi:10.1016/j.jmb.2004.06.088. {{cite journal}}: Check date values in: |date= (help)
^ Thompson, Michael J.; Sievers, Stuart A.; Karanicolas, John; Ivanova, Magdalena I.; Baker, David; Eisenberg, David (2006-03-14). "The 3D profile method for identifying fibril-forming segments of proteins". Proceedings of the National Academy of Sciences. 103 (11): 4074–4078. doi:10.1073/pnas.0511295103. ISSN 0027-8424. PMC 1449648. PMID 16537487.{{cite journal}}: CS1 maint: PMC format (link)
^ Nelson, Rebecca; Sawaya, Michael R.; Balbirnie, Melinda; Madsen, Anders Ø; Riekel, Christian; Grothe, Robert; Eisenberg, David (2005-06). "Structure of the cross-β spine of amyloid-like fibrils". Nature. 435 (7043): 773–778. doi:10.1038/nature03680. ISSN 1476-4687. PMC 1479801. PMID 15944695. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
^ Kuhlman, Brian; Baker, David (2000-09-12). "Native protein sequences are close to optimal for their structures". Proceedings of the National Academy of Sciences. 97 (19): 10383–10388. doi:10.1073/pnas.97.19.10383. ISSN 0027-8424. PMC 27033. PMID 10984534.{{cite journal}}: CS1 maint: PMC format (link)
^ Sawaya, Michael R.; Sambashivan, Shilpa; Nelson, Rebecca; Ivanova, Magdalena I.; Sievers, Stuart A.; Apostol, Marcin I.; Thompson, Michael J.; Balbirnie, Melinda; Wiltzius, Jed J. W.; McFarlane, Heather T.; Madsen, Anders Ø. (2007-05). "Atomic structures of amyloid cross-β spines reveal varied steric zippers". Nature. 447 (7143): 453–457. doi:10.1038/nature05695. ISSN 0028-0836. {{cite journal}}: Check date values in: |date= (help)
^ Galzitskaya, Oxana V.; Garbuzynskiy, Sergiy O.; Lobanov, Michail Yurievich (2006-12-29). "Prediction of Amyloidogenic and Disordered Regions in Protein Chains". PLOS Computational Biology. 2 (12): e177. doi:10.1371/journal.pcbi.0020177. ISSN 1553-7358. PMC 1761655. PMID 17196033.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
^ Zibaee, Shahin; Makin, O. Sumner; Goedert, Michel; Serpell, Louise C. (2007-05). "A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone". Protein Science. 16 (5): 906–918. doi:10.1110/ps.062624507. PMC 2206631. PMID 17456743. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)

[1] Paz, Manuela López de la; Serrano, Luis (2004-01-06). "Sequence determinants of amyloid fibril formation". Proceedings of the National Academy of Sciences. 101 (1): 87–92. doi:10.1073/pnas.2634884100. ISSN 0027-8424. PMC 314143. PMID 14691246.{{cite journal}}: CS1 maint: PMC format (link)

[2] Rousseau, F; Schymkowitz, J; Serrano, L (2006-02). "Protein aggregation and amyloidosis: confusion of the kinds?". Current Opinion in Structural Biology. 16 (1): 118–126. doi:10.1016/j.sbi.2006.01.011. {{cite journal}}: Check date values in: |date= (help)

[3] Fernandez-Escamilla, Ana-Maria; Rousseau, Frederic; Schymkowitz, Joost; Serrano, Luis (2004-10). "Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins". Nature Biotechnology. 22 (10): 1302–1306. doi:10.1038/nbt1012. ISSN 1087-0156. {{cite journal}}: Check date values in: |date= (help)

[4] Linding, Rune; Schymkowitz, Joost; Rousseau, Frederic; Diella, Francesca; Serrano, Luis (2004-09). "A Comparative Study of the Relationship Between Protein Structure and β-Aggregation in Globular and Intrinsically Disordered Proteins". Journal of Molecular Biology. 342 (1): 345–353. doi:10.1016/j.jmb.2004.06.088. {{cite journal}}: Check date values in: |date= (help)

[5] Thompson, Michael J.; Sievers, Stuart A.; Karanicolas, John; Ivanova, Magdalena I.; Baker, David; Eisenberg, David (2006-03-14). "The 3D profile method for identifying fibril-forming segments of proteins". Proceedings of the National Academy of Sciences. 103 (11): 4074–4078. doi:10.1073/pnas.0511295103. ISSN 0027-8424. PMC 1449648. PMID 16537487.{{cite journal}}: CS1 maint: PMC format (link)

[6] Nelson, Rebecca; Sawaya, Michael R.; Balbirnie, Melinda; Madsen, Anders Ø; Riekel, Christian; Grothe, Robert; Eisenberg, David (2005-06). "Structure of the cross-β spine of amyloid-like fibrils". Nature. 435 (7043): 773–778. doi:10.1038/nature03680. ISSN 1476-4687. PMC 1479801. PMID 15944695. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)

[7] Kuhlman, Brian; Baker, David (2000-09-12). "Native protein sequences are close to optimal for their structures". Proceedings of the National Academy of Sciences. 97 (19): 10383–10388. doi:10.1073/pnas.97.19.10383. ISSN 0027-8424. PMC 27033. PMID 10984534.{{cite journal}}: CS1 maint: PMC format (link)

[8] Sawaya, Michael R.; Sambashivan, Shilpa; Nelson, Rebecca; Ivanova, Magdalena I.; Sievers, Stuart A.; Apostol, Marcin I.; Thompson, Michael J.; Balbirnie, Melinda; Wiltzius, Jed J. W.; McFarlane, Heather T.; Madsen, Anders Ø. (2007-05). "Atomic structures of amyloid cross-β spines reveal varied steric zippers". Nature. 447 (7143): 453–457. doi:10.1038/nature05695. ISSN 0028-0836. {{cite journal}}: Check date values in: |date= (help)

[9] Galzitskaya, Oxana V.; Garbuzynskiy, Sergiy O.; Lobanov, Michail Yurievich (2006-12-29). "Prediction of Amyloidogenic and Disordered Regions in Protein Chains". PLOS Computational Biology. 2 (12): e177. doi:10.1371/journal.pcbi.0020177. ISSN 1553-7358. PMC 1761655. PMID 17196033.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)

[10] Zibaee, Shahin; Makin, O. Sumner; Goedert, Michel; Serpell, Louise C. (2007-05). "A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone". Protein Science. 16 (5): 906–918. doi:10.1110/ps.062624507. PMC 2206631. PMID 17456743. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)

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