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 +Table 1MethodLast UpdateAccess (Web server/downloadable)PrincipleInputOutputSequence / 3D StructureAdditional parametersAmyloidogenic Patten2004Web Server- AMYLPRED2Secondary 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 2004Web Server-TANGOPhenomenological Based on physico-chemical principles of secondary structure formation extended by the assumption that the core regions of an aggregate are fully buried.sequencepH/ionic strengthOverall aggregation and amyloidoidogenic regionsAverage Packing Density2006Web Server-AMYLPRED2Secondary structure-related Relates average packing density of residues to the formation of amyloid fibrils.sequence -Amyloidogenic regions Beta-strand contiguity2007Web Server- AMYLPRED2Phenomenological Prediction of B-strand propensity score to locate in the amyloid fibril. sequence -beta-strand formationHexapeptide Conformational Energy /Pre-amyl2007Web Server- AMYLPRED2Secondary 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 energyAGGRESCAN2007Web Servers -AMLYPRED2 & AGGRESCANPhenomenological 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 Salsa2007Web server - AMYPdbPhenomenological Prediction of the aggregation propensities single or multiple sequences based on physicochemical properties.sequencehot spot lengthAmyloidogenic regions Pafig2009Web server- AMYLPRED2 DownloadPhenomenological Identification of Hexapeptides associated to amyloid fibrillar aggregates.sequence -Amyloidogenic regions Net-CSSP2020Web Server - Net-CSSP AMYLPRED2Secondary structure-related Quantification of the influence of the tertiary interation on secondary structural preference.sequence/pdbsingle/dual network-thresholdAmyloidogenic propensity regions Betascan2009Web Server - Betascan Download - Betascan Secondary structure-related Predict the probability that particular portions of a protein will form amyloid.sequencelengthAmyloidogenic regions FoldAmyloid2010Web Server - FoldAmyloidSecondary structure-related Prediction of amyloid regions using expected probability of hydrogen bonds formation and packing densitites of residues.sequencescale, threshold, averaging frameAmyloidogenic regions Waltz2010Web Server - Waltz & AMYLPRED2Secondary structure-related Application of position-specific substitution matrices (PSSM) obtained from amyloidogenic peptides.sequencepH, specificity, sensitivityAmyloidogenic regions Zipper DB 2010Web Server- Zipper DBSecondary 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 conformationSTITCHER2012 Web Server - Stitcher (currently offline)Secondary structure-relatedsequence -Amyloidogenic regions MetAmyl2013Web Server - MetAmylConsensus method Amyloidogenic patterns, average packing density, beta-strand contiguity, pafig, Net-CSSP, STITCHERsequencethresholdOverall generic and amyloidogenic regions based on the consensus AmylPred22013Web Server - AMYLPRED2Consensus method Amyloidogenic patterns, average packing density, beta-strand contiguity, pafig, Net-CSSP, STITCHERsequence -Overall generic and amyloidogenic regions based on the consensus PASTA 2.02014Web Server - PASTA 2.0Secondary structure-related Predicts the most aggregation-prone portions and the corresponding β-strand inter-molecular pairing for multiple input sequences.sequencetop pairings and energies, mutations and protein-proteinAmyloidogenic regions, energy, and beta-sheet orientation in aggregates FISH Amyloid2014Web Server - Comprec (currently offline)Secondary structure-relatedsequencethresholdAmyloidogenic regions GAP2014Web Server - GAPSecondary 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 APPNN2015Download - CRANPhenomenological 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 ArchCandy2015Download- BiSMMSecondary structure-related Based on an assumption that protein sequences that are able to form β-arcades are amyloidogenic.sequence -Amyloidogenic regions Amyload2015Web Server - Comprec (currently offline) Consensus methodsequence -Overall generic and amyloidogenic regions SolubiS2016Web Server - SolubiS3D structurepdb filechain, threshold, gatekeeperAggregation propensity and stability vs mutationsCamSol Structurally Corrected2017Web Server - Chemistry of Health3D structurepdb filepH, patch radiusExposed aggregation-prone patches and mutated variants designCamSol intrinsic2017Web Server- Chemistry of HealthPhenomenological Sequence-based method of predicting protein solubility and generic aggregation propensity.sequencepHCalculation of the overall intrinsic solubility score and solubility profileAmyloGram2017Web Server - AmyloGramPhenomenological AmyloGram predicts amyloid proteins using n-gram encoding and random forests.sequence -Overall aggregation and amyloidogenic regionsBetaSerpentine2017Web Server - BetaSerpentine-1.0Sequence-related Reconstruction of amyloid structures containing adjacent β-arches.sequence -Amyloidogenic regionsAggScore2018AggScore is available through 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-Pred2018Web Server - AggreRAE-PredSecondary structure-related Predict changes in aggregation rate upon point mutationssequence pdbmutationsAGGRESCAN 3D 2.02019Web Server - Aggrescan3D3D structurepdb filedynamic mode, mutations, patch radius, stability, enhance solubilityDynamic exposed aggregation-prone patches and mutated variants designBudapest amyloid predictor2021Web Server - Budapest amyloid predictorHexapeptidesequenceAmyloidgenecity of hexapeptideANuPP2021Web Server - ANuPPHexapeptide and Sequence Identification amyloid-fibril forming peptides and regions in protein sequencessequenceAmyloidogenic hexapeptides and aggregation prone regions

See also PhasAGE toolbox

Amyloid

Protein aggregation

References