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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.

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

Downloadable

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
PAGE?? 2009 - Structure-related sequence - Generic or beta-aggregation prone 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
SAP?? 2009 - 3D structure pdb file - Dynamic exposed hydrophobic pathces
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 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

  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)
  11. ^ Zhang, Zhuqing; Chen, Hao; Lai, Luhua (2007-09-01). "Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential". Bioinformatics. 23 (17): 2218–2225. doi:10.1093/bioinformatics/btm325. ISSN 1367-4803.
  12. ^ Sormanni, Pietro; Aprile, Francesco A.; Vendruscolo, Michele (2015-01). "The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility". Journal of Molecular Biology. 427 (2): 478–490. doi:10.1016/j.jmb.2014.09.026. {{cite journal}}: Check date values in: |date= (help)
  13. ^ Sormanni, Pietro; Amery, Leanne; Ekizoglou, Sofia; Vendruscolo, Michele; Popovic, Bojana (2017-12). "Rapid and accurate in silico solubility screening of a monoclonal antibody library". Scientific Reports. 7 (1): 8200. doi:10.1038/s41598-017-07800-w. ISSN 2045-2322. {{cite journal}}: Check date values in: |date= (help)
  14. ^ Conchillo-Solé, Oscar; de Groot, Natalia S.; Avilés, Francesc X.; Vendrell, Josep; Daura, Xavier; Ventura, Salvador (2007-02-27). "AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides". BMC Bioinformatics. 8 (1): 65. doi:10.1186/1471-2105-8-65. ISSN 1471-2105. PMC 1828741. PMID 17324296.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  15. ^ Zibaee, Shahin; Makin, O. Sumner; Goedert, Michel; Serpell, Louise C. (2007). "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. ISSN 1469-896X. PMC 2206631. PMID 17456743.{{cite journal}}: CS1 maint: PMC format (link)
  16. ^ Pawlicki, Sandrine; Le Béchec, Antony; Delamarche, Christian (2008-06-10). "AMYPdb: A database dedicated to amyloid precursor proteins". BMC Bioinformatics. 9 (1): 273. doi:10.1186/1471-2105-9-273. ISSN 1471-2105. PMC 2442844. PMID 18544157.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  17. ^ Tian, Jian; Wu, Ningfeng; Guo, Jun; Fan, Yunliu (2009-01-30). "Prediction of amyloid fibril-forming segments based on a support vector machine". BMC Bioinformatics. 10 (1): S45. doi:10.1186/1471-2105-10-S1-S45. ISSN 1471-2105. PMC 2648769. PMID 19208147.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  18. ^ Kim, C.; Choi, J.; Lee, S. J.; Welsh, W. J.; Yoon, S. (2009-07-01). "NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation". Nucleic Acids Research. 37 (Web Server): W469 – W473. doi:10.1093/nar/gkp351. ISSN 0305-1048. PMC 2703942. PMID 19468045.{{cite journal}}: CS1 maint: PMC format (link)
  19. ^ Yoon, Sukjoon; Welsh, William J.; Jung, Heeyoung; Yoo, Young Do (2007-10). "CSSP2: An improved method for predicting contact-dependent secondary structure propensity". Computational Biology and Chemistry. 31 (5–6): 373–377. doi:10.1016/j.compbiolchem.2007.06.002. {{cite journal}}: Check date values in: |date= (help)
  20. ^ Yoon, Sukjoon; Welsh, William J. (2005-04-22). "Rapid assessment of contact-dependent secondary structure propensity: Relevance to amyloidogenic sequences". Proteins: Structure, Function, and Bioinformatics. 60 (1): 110–117. doi:10.1002/prot.20477.
  21. ^ Yoon, Sukjoon; Welsh, William J. (2004-08). "Detecting hidden sequence propensity for amyloid fibril formation". Protein Science. 13 (8): 2149–2160. doi:10.1110/ps.04790604. ISSN 0961-8368. {{cite journal}}: Check date values in: |date= (help)
  22. ^ Jr, Allen W. Bryan; Menke, Matthew; Cowen, Lenore J.; Lindquist, Susan L.; Berger, Bonnie (2009-03-27). "BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis". PLOS Computational Biology. 5 (3): e1000333. doi:10.1371/journal.pcbi.1000333. ISSN 1553-7358. PMC 2653728. PMID 19325876.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  23. ^ Garbuzynskiy, S. O.; Lobanov, M. Yu.; Galzitskaya, O. V. (2010-02-01). "FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence". Bioinformatics. 26 (3): 326–332. doi:10.1093/bioinformatics/btp691. ISSN 1367-4803.
  24. ^ Oliveberg, Mikael (2010-03). "Waltz, an exciting new move in amyloid prediction". Nature Methods. 7 (3): 187–188. doi:10.1038/nmeth0310-187. ISSN 1548-7091. {{cite journal}}: Check date values in: |date= (help)
  25. ^ Maurer-Stroh, Sebastian; Debulpaep, Maja; Kuemmerer, Nico; de la Paz, Manuela Lopez; Martins, Ivo Cristiano; Reumers, Joke; Morris, Kyle L.; Copland, Alastair; Serpell, Louise; Serrano, Luis; Schymkowitz, Joost W. H. (2010-03). "Exploring the sequence determinants of amyloid structure using position-specific scoring matrices". Nature Methods. 7 (3): 237–242. doi:10.1038/nmeth.1432. ISSN 1548-7105. {{cite journal}}: Check date values in: |date= (help)
  26. ^ Bryan, Allen W.; O'Donnell, Charles W.; Menke, Matthew; Cowen, Lenore J.; Lindquist, Susan; Berger, Bonnie (2012-02). "STITCHER: Dynamic assembly of likely amyloid and prion β‐structures from secondary structure predictions". Proteins: Structure, Function, and Bioinformatics. 80 (2): 410–420. doi:10.1002/prot.23203. ISSN 0887-3585. PMC 3298606. PMID 22095906. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  27. ^ Tian, Jian; Wu, Ningfeng; Guo, Jun; Fan, Yunliu (2009-01). "Prediction of amyloid fibril-forming segments based on a support vector machine". BMC Bioinformatics. 10 (S1): S45. doi:10.1186/1471-2105-10-S1-S45. ISSN 1471-2105. PMC 2648769. PMID 19208147. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  28. ^ 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)
  29. ^ Maurer-Stroh, Sebastian; Debulpaep, Maja; Kuemmerer, Nico; de la Paz, Manuela Lopez; Martins, Ivo Cristiano; Reumers, Joke; Morris, Kyle L; Copland, Alastair; Serpell, Louise; Serrano, Luis; Schymkowitz, Joost W H (2010-03). "Exploring the sequence determinants of amyloid structure using position-specific scoring matrices". Nature Methods. 7 (3): 237–242. doi:10.1038/nmeth.1432. ISSN 1548-7091. {{cite journal}}: Check date values in: |date= (help)
  30. ^ Garbuzynskiy, S. O.; Lobanov, M. Yu.; Galzitskaya, O. V. (2010-02-01). "FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence". Bioinformatics. 26 (3): 326–332. doi:10.1093/bioinformatics/btp691. ISSN 1367-4803.
  31. ^ Tsolis, Antonios C.; Papandreou, Nikos C.; Iconomidou, Vassiliki A.; Hamodrakas, Stavros J. (2013-01-10). "A Consensus Method for the Prediction of 'Aggregation-Prone' Peptides in Globular Proteins". PLOS ONE. 8 (1): e54175. doi:10.1371/journal.pone.0054175. ISSN 1932-6203. PMC 3542318. PMID 23326595.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  32. ^ Walsh, Ian; Seno, Flavio; Tosatto, Silvio C.E.; Trovato, Antonio (2014-05-21). "PASTA 2.0: an improved server for protein aggregation prediction". Nucleic Acids Research. 42 (W1): W301 – W307. doi:10.1093/nar/gku399. ISSN 1362-4962. PMC 4086119. PMID 24848016.{{cite journal}}: CS1 maint: PMC format (link)
  33. ^ Gasior, Pawel; Kotulska, Malgorzata (2014-12). "FISH Amyloid – a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids". BMC Bioinformatics. 15 (1): 54. doi:10.1186/1471-2105-15-54. ISSN 1471-2105. PMC 3941796. PMID 24564523. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  34. ^ Thangakani, A. Mary; Kumar, Sandeep; Nagarajan, R.; Velmurugan, D.; Gromiha, M. Michael (2014-03-28). "GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies". Bioinformatics. 30 (14): 1983–1990. doi:10.1093/bioinformatics/btu167. ISSN 1460-2059.
  35. ^ Thangakani, Anthony Mary; Kumar, Sandeep; Velmurugan, Devadasan; Gromiha, Maria Siluvay Michael (2012-04). "How do thermophilic proteins resist aggregation?". Proteins: Structure, Function, and Bioinformatics. 80 (4): 1003–1015. doi:10.1002/prot.24002. {{cite journal}}: Check date values in: |date= (help)
  36. ^ Gromiha, M. Michael; Thangakani, A. Mary; Kumar, Sandeep; Velmurugan, D. (2012), Huang, De-Shuang; Gupta, Phalguni; Zhang, Xiang; Premaratne, Prashan (eds.), "Sequence Analysis and Discrimination of Amyloid and Non-amyloid Peptides", Emerging Intelligent Computing Technology and Applications, vol. 304, Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 447–452, doi:10.1007/978-3-642-31837-5_65, ISBN 978-3-642-31836-8, retrieved 2021-11-26
  37. ^ Thangakani, A Mary; Kumar, Sandeep; Velmurugan, D; Gromiha, M Michael (2013-05). "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". BMC Bioinformatics. 14 (S8): S6. doi:10.1186/1471-2105-14-S8-S6. ISSN 1471-2105. PMC 3654898. PMID 23815227. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  38. ^ Thangakani, A. Mary; Kumar, Sandeep; Nagarajan, R.; Velmurugan, D.; Gromiha, M. Michael (2014-03-28). "GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies". Bioinformatics. 30 (14): 1983–1990. doi:10.1093/bioinformatics/btu167. ISSN 1460-2059.
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