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  • Prabakaran R, IIT Madras

  • Puneet Rawat, IIT Madras

  • Dr. Sandeep Kumar, Boehringer Ingelheim

  • Prof. M. Michael Gromiha, IIT Madras

Cite us:

  • Prabakaran R, Puneet Rawat, Sandeep Kumar and M. Michael Gromiha (2021) ANuPP: A versatile tool to predict aggregation nucleating regions in proteins. Journal of Molecular Biology, 433(1), 166707. link
  • Rawat,P. et al. (2020) CPAD 2.0: a repository of curated experimental data on aggregating proteins and peptides. Amyloid, 16.
  • Prabakaran,R. et al. (2017a) Aggregation prone regions in human proteome: In-sights from large-scale data analyses. Proteins Struct. Funct. Bioinforma., 85, 10991118.
  • Prabakaran,R. et al. (2017b) Influence of Amino Acid Properties for Characterizing Amyloid Peptides in Human Proteome. Lecture Notes in Computer Sci-ence, 10362. Springer, Cham.
  • Thangakani,A.M. et al. (2016) CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation. PLoS One, 11, e0152949.
  • Thangakani,A.M. et al. (2014) GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies. Bioinformatics, 30, 19831990.


  • Agostini,F. et al. (2014) ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli. Bioinformatics, 30, 29752977.
  • Ahmed,A.B. et al. (2015) A structure-based approach to predict predisposition to amyloidosis. Alzheimer’s Dement., 11, 681690.
  • Beerten,J. et al. (2014) WALTZ-DB: A benchmark database of amyloidogenic hexapeptides. Bioinformatics, 31, 16981700.
  • Bryan,A.W. et al. (2009) BETASCAN: Probable beta-amyloids Identified by Pair-wise Probabilistic Analysis. PLoS Comput. Biol., 5, e1000333.
  • Conchillo-Solé,O. et al. (2007) AGGRESCAN: a server for the prediction and evaluation of ‘hot spots’ of aggregation in polypeptides. BMC Bioinformat-ics, 8, 65.
  • Fernandez-Escamilla,A.-M. et al. (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat. Biotech-nol., 22, 13026.
  • Galzitskaya,O. V. et al. (2006) Prediction of amyloidogenic and disordered re-gions in protein chains. PLoS Comput. Biol., 2, 16391648.
  • Gasior, P. and Kotulska, M. (2014) FISH Amyloid a new method for finding amyloidogenic segments in proteins based on site specific co-occurrence of amino acids. BMC Bioinformatics, 15, 54.
  • Hamodrakas,S.J. et al. (2007) Consensus prediction of amyloidogenic determi-nants in amyloid fibril-forming proteins. Int. J. Biol. Macromol., 41, 295300.
  • Maurer-Stroh,S. et al. (2010) Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat. Methods, 7, 237242.
  • Palato,L.M. et al. (2019) Amyloidogenicity of naturally occurring full-length animal IAPP variants. J. Pept. Sci., 25, 18.
  • Pastor,M.T. et al. (2007) Hacking the code of amyloid formation: the amyloid stretch hypothesis. Prion, 1, 914.
  • López de la Paz,M. and Serrano,L. (2004) Sequence determinants of amyloid fibril formation. Proc. Natl. Acad. Sci. U. S. A., 101, 8792.
  • Rose,A.S. et al. (2018) NGL viewer: web-based molecular graphics for large complexes. Bioinformatics, 34, 37553758.
  • Saelices,L. et al. (2018) Crystal structures of amyloidogenic segments of human transthyretin. Protein Sci., 27, 1295-1303.
  • Saelices,L. et al. (2015) Uncovering the mechanism of aggregation of human transthyretin. J. Biol. Chem., 290, 2893228943.
  • Tartaglia,G.G. et al. (2005) Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci., 14, 27232734.
  • Tian,J. et al. (2009) Prediction of amyloid fibril-forming segments based on a support vector machine. BMC Bioinformatics, 10, S45.
  • Tsolis,A.C. et al. (2013) A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins. PLoS One, 8, e54175.
  • Varadi,M. et al. (2017) AmyPro: a database of proteins with validated amyloido-genic regions. Nucleic Acids Res., 46, D387-D392.
  • Walsh,I. et al. (2014) PASTA 2.0: An improved server for protein aggregation prediction. Nucleic Acids Res., 42, 301307.
  • Wozniak,P.P. and Kotulska,M. (2015) AmyLoad: Website dedicated to amyloidogenic protein fragments. Bioinformatics, 31, 33953397.
  • Zambrano,R. et al. (2015) AGGRESCAN3D (A3D): Server for prediction of aggregation properties of protein structures. Nucleic Acids Res., 43, W306W313.
  • Zhang Z, Chen H, Lai L (2007) Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential. Bioinformatics 23: 22182225.