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Protocols

ProtoNet specifications

Information


Unique identifier OMICS_03876
Name ProtoNet
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 6.1
Maintained Yes

Maintainer


  • person_outline Michal Linial

Publication for ProtoNet

ProtoNet citations

 (18)
library_books

Gene regulation in Kluyveromyces marxianus in the context of chromosomes

2018
PLoS One
PMCID: 5773181
PMID: 29346402
DOI: 10.1371/journal.pone.0190913

[…] and KLMA_10523 was considered.Gene KLMA_10520 has the GO terms "FMN binding [GO:0010181] and oxidoreductase activity [GO:0016491]" associated on the UniProt database. For gene KLMA_10523, a search on ProtoNet [] suggested that the protein may bind to the enzyme protein phosphatase type 1, based on structural similarity with other proteins in its protein structural cluster from various species, inc […]

call_split

Small Myristoylated Protein 3, Identified as a Potential Virulence Factor in Leishmania amazonensis, Proves to be a Protective Antigen against Visceral Leishmaniasis

2018
Int J Mol Sci
PMCID: 5796078
PMID: 29301342
DOI: 10.3390/ijms19010129
call_split See protocol

[…] nt in the non-classical secretory pathway. TMHMM [] was used to predict a molecule as a membrane protein, whereas the protein functional domain was predicted by SUPERFAMILY [], CATH [], SMART [], and ProtoNet 6.0 [] servers. Receiver Operator Characteristics (ROC) curves were constructed to evaluate the subcellular localization and to predict biological functions. Results were shown as sensitivity […]

library_books

Sequence Analysis of Hypothetical Proteins from Helicobacter pylori 26695 to Identify Potential Virulence Factors

2016
PMCID: 5056897
PMID: 27729842
DOI: 10.5808/GI.2016.14.3.125

[…] arch may give ample evidence for function prediction of the HPs. We have used an array of databases and retrieval tools such as CATH [], SUPERFAMILY [], PANTHER [], Pfam [], CDART [], SVMProt [], and ProtoNet [] for the classification of the HPs. CATH provides the classification of Protein Data Bank (PDB) protein structure repository. CATH v4.0 release contains 235,858 domains, 2,738 superfamily a […]

library_books

Identification of Functional Candidates amongst Hypothetical Proteins of Treponema pallidum ssp. pallidum

2015
PLoS One
PMCID: 4403809
PMID: 25894582
DOI: 10.1371/journal.pone.0124177

[…] tein. Furthermore, Pfam database was used to predict the function of proteins based on sequence similarity. We have also performed protein classification using clustering techniques using SYSTERS and ProtoNet. SYSTERS is a database of protein family which uses BLASTp to search the database for similar sequences and provides the cluster of proteins formed on the basis of functional similarity. Howe […]

library_books

Structure based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae

2014
3 Biotech
PMCID: 4569619
PMID: 28324524
DOI: 10.1007/s13205-014-0274-1

[…] [47]. The databases such as Pfam (Punta et al. ), PANTHER (Mi et al. ), SMART (Letunic et al. ), SUPERFAMILY (Gough et al. ), CATH (Sillitoe et al. ), CDART (Geer et al. ), SYSTERS (Meinel et al. ), ProtoNet (Rappoport et al. ) and SVMProt (Cai et al. ) were used for precise domain annotation in HPs. Similarly, instead of direct sequence similarity, we also used domain architecture and profile-ba […]

library_books

Structure based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae

2014
3 Biotech
PMCID: 4434415
PMID: 28324295
DOI: 10.1007/s13205-014-0231-z

[…] By applying the clustering algorithms, we analyzed that HP P44717 is a member of cluster 143846 (CBS domain protein) of SYSTERS (Meinel et al. ) and cluster 4144744 (Transporter-associated region) of ProtoNet (Rappoport et al. ), and a member of transmembrane family protein. Sequence-based motifs are discovered using InterProScan (Quevillon et al. ) and MOTIF tools (Kanehisa ). We further observed […]

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ProtoNet institution(s)
School of Computer Science and Engineering, The Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, Israel; Deptartment of Biological Chemistry, Institute of Life Sciences, The Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, Israel
ProtoNet funding source(s)
Supported by Sudarsky Center for Computational Biology (SCCB) fellowship, EU FRVII Prospects consortium and the Israel Science Foundation ISF 592/07.

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