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PASTA specifications

Information


Unique identifier OMICS_03861
Name PASTA
Alternative name Prediction of Amyloid StrucTure Aggregation
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Some single or multiple sequences.
Input format FASTA
Programming languages C
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Silvio Tosatto

Additional information


http://protein.bio.unipd.it/pasta2/help.html http://protein.bio.unipd.it/pasta2/about.html

Information


Unique identifier OMICS_03861
Name PASTA
Alternative name Prediction of Amyloid StrucTure Aggregation
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Silvio Tosatto

Additional information


http://protein.bio.unipd.it/pasta2/help.html http://protein.bio.unipd.it/pasta2/about.html

Publications for Prediction of Amyloid StrucTure Aggregation

PASTA citations

 (36)
library_books

Using extensional flow to reveal diverse aggregation landscapes for three IgG1 molecules

2018
Biotechnol Bioeng
PMCID: 5900942
PMID: 29315487
DOI: 10.1002/bit.26543

[…] ). In silico analyses, such as TANGO (Fernandez‐Escamilla, Rousseau, Schymkowitz, & Serrano, ), Zyggregator (Tartaglia & Vendruscolo, ), Waltz (Oliveberg, ), Aggrescan (Conchillo‐Solé et al., ), and PASTA (Trovato, Seno, & Tosatto, ) can be used to predict the presence of aggregation‐prone regions (APRs) within proteins using protein primary sequence information alone. In addition, CamSol (Sorman […]

library_books

Engineering of Fc Fragments with Optimized Physicochemical Properties Implying Improvement of Clinical Potentials for Fc Based Therapeutics

2018
Front Immunol
PMCID: 5766897
PMID: 29375551
DOI: 10.3389/fimmu.2017.01860

[…] ed after rational introduction of proper hydrophilic amino acids for disruption of the large hydrophobic aggregation-prone clusters. In addition to SAP (–), several online programs such as TANGO (–), PASTA (), AGGRESCAN (), and Aggrescan3D () are also widely used to predict aggregation-prone regions within proteins. Therefore, it is desired that new Ig variants could be identified in the future.In […]

call_split

Candida albicans Sap6 amyloid regions function in cellular aggregation and zinc binding, and contribute to zinc acquisition

2017
Sci Rep
PMCID: 5460171
PMID: 28588252
DOI: 10.1038/s41598-017-03082-4
call_split See protocol

[…] or specifically designed, to predict features related to the formation of amyloid fibrils. Each predicted amyloidogenic regions from Sap6 was further confirmed using TANGO (http://tango.crg.es/) and PASTA 2.0(http://protein.bio.unipd.it/pasta2/), . […]

library_books

Prediction and Reduction of the Aggregation of Monoclonal Antibodies

2017
J Mol Biol
PMCID: 5397608
PMID: 28322916
DOI: 10.1016/j.jmb.2017.03.014

[…] ilable human sequences from the abYsis database were acquired and properties like charge distribution, hydrophobicity, statistical sequence scores , CDR-specific properties, and aggregation tendency (PASTA ) were computed. For each of these properties, a distribution was obtained and antibodies were selected that were extreme in at least one property and had an X-ray structure or a close homology […]

library_books

Contact dependent killing by Caulobacter crescentus via cell surface associated, glycine zipper proteins

2017
eLife
PMCID: 5380434
PMID: 28323618
DOI: 10.7554/eLife.24869.022

[…] y and amylogenic regions of CdzC, CdzD and CdzI were predicted based on amino acid sequence using AmylPred 2 (), WALZ (high specificity threshold) (), MetAmyl (with high specificity threshold) () and PASTA 2.0 (with peptides threshold) (). A sequence region was considered aggregation prone if at least three of the above algorithms were in accordance.To identify CdzC/D-like proteins in other organi […]

call_split

Investigating Mutations to Reduce Huntingtin Aggregation by Increasing Htt N Terminal Stability and Weakening Interactions with PolyQ Domain

2016
PMCID: 5206856
PMID: 28096892
DOI: 10.1155/2016/6247867
call_split See protocol

[…] the 3-point mutations that are both stable and least amyloidogenic, which would result in slower amyloid formation and slower disease progression. In particular, we use Zyggregator [], TANGO [], and PASTA [] to predict the aggregation propensities of the top ranking stable 3-point mutations. The top 3 mutations with best stability and lowest amyloidogenicity were run through an MD production to v […]

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PASTA institution(s)
Department of Biomedical Sciences, University of Padova, Padova, Italy; INFN, Padova Section, and Department of Physics and Astronomy 'G Galilei', University of Padova, Padova, Italy
PASTA funding source(s)
Supported by Padova University through Progetto di Ateneo [CPDA121890]; Italian Ministry for University and Research through FIRB Futuro in Ricerca [RBFR08ZSXY].

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