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Protocols

ModPred specifications

Information


Unique identifier OMICS_09201
Name ModPred
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Predrag Radivojac

Information


Unique identifier OMICS_09201
Name ModPred
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Predrag Radivojac

Publication for ModPred

ModPred citations

 (6)
library_books

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder Enriched Interactions

2017
Int J Mol Sci
PMCID: 5751360
PMID: 29257115
DOI: 10.3390/ijms18122761

[…] beyond the analysis based on ELMs that focuses specially on the PTMs associated with SLiMs, by encompassing a broader set of PTMs and quantifying 21 specific PTM types. We annotated the PTMs with the ModPred software [] that is tuned for eukaryotic organisms. The considered PTM types include acetylation, ADP-ribosylation, amidation, carboxylation, C-linked glycosylation, farnesylation, geranylgera […]

library_books

Identification and Initial Characterization of the Effectors of an Anther Smut Fungus and Potential Host Target Proteins

2017
Int J Mol Sci
PMCID: 5713455
PMID: 29165363
DOI: 10.3390/ijms18112489

[…] biological sequences employed Basic Local Alignment Search Tool (BLAST; https://blast.ncbi.nlm.nih.gov/Blast.cgi). Further domain analysis for prediction of post translational modification sites used ModPred []. Structural modelling of predicted proteins utilized Swiss-Model [,]. Results of these analyses are found in . Additional analysis methods are provided in and associated references [,,,]. […]

library_books

Protein post translational modifications: In silico prediction tools and molecular modeling

2017
Comput Struct Biotechnol J
PMCID: 5397102
PMID: 28458782
DOI: 10.1016/j.csbj.2017.03.004

[…] of PTM sites in the proteins. In this emerging context, computational methods are poised to support the study of PTM cross-talk. The first unified tool for a simultaneous prediction of PTM sites was ModPred , which predicts and analyses simultaneously multiple types of PTM sites in order to gain structural and functional information on the protein regulatory mechanism of multiple PTMs. Recently, […]

call_split

Two Isoforms of Yersinia pestis Plasminogen Activator Pla: Intraspecies Distribution, Intrinsic Disorder Propensity, and Contribution to Virulence

2016
PLoS One
PMCID: 5148098
PMID: 27936190
DOI: 10.1371/journal.pone.0168089
call_split See protocol

[…] be identified by various computational means, such as the ANCHOR algorithm [, ]. Also, since intrinsic disorder is intimately linked to various posttranslational modifications (PTMs) [–], we used the ModPred tool [] to evaluate how the I259T polymorphism affects the predisposition of the Pla C-terminal region for being posttranslationally modified. […]

library_books

Lipopolysaccharide treatment induces genome wide pre mRNA splicing pattern changes in mouse bone marrow stromal stem cells

2016
BMC Genomics
PMCID: 5001229
PMID: 27557078
DOI: 10.1186/s12864-016-2898-5

[…] t undergo a disorder–order transformation while binding another protein molecule []. Known post-translational modification (PTM) sites were derived from UniProt, and novel PTM sites were predicted by ModPred []. The upstream gene regulator NFYA (Nuclear transcription Factor Y subunit Alpha) [] was predicted by Ingenuity Pathway Analysis (IPA), based on gene expression data and known regulatory gen […]

call_split

Prothymosin α Variants Elicit Anti HIV 1 Response via TLR4 Dependent and Independent Pathways

2016
PLoS One
PMCID: 4910978
PMID: 27310139
DOI: 10.1371/journal.pone.0156486
call_split See protocol

[…] PTM sites in different ProTα variants were identified using a unified sequence-based predictor of 23 types of PTM sites that is available at www.modpred.org []. Only sites predicted to be modified with high confidence (possessing score ≥0.9) were considered in this study. […]

Citations

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ModPred institution(s)
Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana; Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana; Industrial Internet Laboratory, General Electric Software Center, General Electric Global Research, San Ramon, California; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, University of South Florida, Tampa, Florida; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia

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