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Aggregation prediction software tools | Protein structure data analysis

Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series…
TANGO
Desktop

TANGO

A computer algorithm to predict aggregation nucleating regions in proteins as…

A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions.

Zyggregator
Web

Zyggregator

This web app helps to predict the aggregation propensities of polypeptide…

This web app helps to predict the aggregation propensities of polypeptide chains based on their amino acid sequences. Zyggregator uses the fact that the sequence of a protein determines its behaviour…

Waltz
Web

Waltz

A web app which uses a position-specific scoring matrix to determine…

A web app which uses a position-specific scoring matrix to determine amyloid-forming sequences. Waltz allows users to identify and better distinguish between amyloid sequences and amorphous…

ArchCandy
Desktop

ArchCandy

Allows searching candidates (“candies”) capable of forming stacks of…

Allows searching candidates (“candies”) capable of forming stacks of β-arches. ArchCandy can explore the human proteome (over 21 000) and uses positive (composed of 23 proteins and peptides…

AGGRESCAN
Web

AGGRESCAN

A simple and fast algorithm that predicts aggregation-prone segments in protein…

A simple and fast algorithm that predicts aggregation-prone segments in protein sequences, compares the aggregation properties of different proteins or protein sets and analyses the effect of…

PASTA
Web

PASTA Prediction of Amyloid StrucTure Aggregation

An algorithm to predict the most aggregation-prone portions and the…

An algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence.

NetCSSP
Web
Fibpredictor
Desktop

Fibpredictor

Generates structural models for any amyloid fibril, starting from its sequence.…

Generates structural models for any amyloid fibril, starting from its sequence. Fibpredictor is a computational procedure that identifies energetically favorable class of amyloid fibril for a peptide…

BETASCAN
Desktop
Web

BETASCAN

Calculates likelihood scores for potential beta-strands and strand-pairs based…

Calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets.

A3D
Web

A3D AGGRESCAN3D

A server for prediction of aggregation propensity in protein structures and…

A server for prediction of aggregation propensity in protein structures and rational design of protein solubility. In dynamic mode, A3D takes into account the flexibility of natural and designed…

APPNN
Desktop

APPNN Amyloid propensity prediction neural network

An amyloidogenicity propensity predictor based on a machine learning approach…

An 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…

GAP
Web

GAP Generalized Aggregation Proneness

Discriminating between Amyloid forming peptide and Amorphous Beta Aggregate.

Discriminating between Amyloid forming peptide and Amorphous Beta Aggregate.

AMYLPRED
Web

AMYLPRED

It employs a consensus of different methods that have been found or…

It employs a consensus of different methods that have been found or specifically developed to predict features related to the formation of amyloid fibrils.

BetaSerpentine
Web
Desktop

BetaSerpentine

Allows reconstruction of s β-serpentine arrangements from individual…

Allows reconstruction of s β-serpentine arrangements from individual β-arches. BetaSerpentine predicts possible β-serpentine arrangements of adjacent β-arches and ranks them based on the newly…

AmyLoad
Web

AmyLoad

Collects the amyloidogenic sequences from all major sources. AmyLoad allows for…

Collects the amyloidogenic sequences from all major sources. AmyLoad allows for filtration of the fragments and provides detailed information about each of them. Registered users can both personalize…

Solubis
Desktop

Solubis

Automates the process of carefully selecting point mutations that minimize the…

Automates the process of carefully selecting point mutations that minimize the intrinsic aggregation propensity whilst improving local protein stability. This plugin combines TANGO, FoldX and YASARA.

SOLpro
Desktop
Web

SOLpro

Predicts the propensity of a protein to be soluble upon overexpression in E.…

Predicts the propensity of a protein to be soluble upon overexpression in E. coli using a two-stage SVM architecture based on multiple representations of the primary sequence. Each classifier of the…

FoldAmyloid
Web

FoldAmyloid

Prediction of amyloidogenic regions in the protein chain.

Prediction of amyloidogenic regions in the protein chain.

FISH Amyloid
Web

FISH Amyloid

A machine learning method for classification of aminoacid sequences, based on…

A machine learning method for classification of aminoacid sequences, based on discovering a segment with a discriminative pattern of site-specific co-occurrences between sequence elements.

MetAmyl
Web

MetAmyl

A meta-predictor for hot spots prediction for METapredictor for AMYLoid…

A meta-predictor for hot spots prediction for METapredictor for AMYLoid proteins.

Pafig
Desktop

Pafig Prediction of amyloid fibril-forming segments

A method based on support vector machines, to identify the hexpeptides…

A method based on support vector machines, to identify the hexpeptides associated with amyloid fibrillar aggregates.

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