MOTIPS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MOTIPS
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Tool usage distribution map

This map represents all the scientific publications referring to MOTIPS per scientific context
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Protocols

MOTIPS specifications

Information


Unique identifier OMICS_30224
Name MOTIPS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Hugo Lam

Publications for MOTIPS

MOTIPS citations

 (5)
library_books

TORC2 dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids

2014
eLife
PMCID: 4217029
PMID: 25279700
DOI: 10.7554/eLife.03779.015

[…] t matrix defining Ypk1 phosphoacceptor site specificity was made merging previously published data sets defining Ypk1 primary sequence specificity (; ). This position weight matrix was then used with MOTIPS () to identify proteins with likely phosphorylated occurrences of this motif. Yeastmine () was used to identify all S. cerevisiae genes that showed genetic interactions with Ypk1, Ypk2, any com […]

library_books

Network Evolution: Rewiring and Signatures of Conservation in Signaling

2012
PLoS Comput Biol
PMCID: 3305342
PMID: 22438796
DOI: 10.1371/journal.pcbi.1002411

[…] The set of target binding sites, linear peptide sequences, for each SH3 and kinase domain were provided by the MOTIPS pipeline. When multiple target binding sites overlap, a target binding site cluster is formed. Specifically, a binding site cluster is defined as a region on a protein target for which every pe […]

library_books

Evaluation and Properties of the Budding Yeast Phosphoproteome*

2012
PMCID: 3433898
PMID: 22286756
DOI: 10.1074/mcp.M111.009555

[…] ein kinases (61/122). By integrating these sequence motifs together with other features, such as evolutionary conservation, disorder and protein surface accessibility, they used a Bayesian algorithm (MOTIPS) to predict phosphorylation sites for certain kinases. By applying a likelihood threshold of >0.5, we observed that MOTIPS could assign a kinase to 34% (165/480) p-sites in PhosphoGrid, 40% (10 […]

library_books

Measuring the Evolutionary Rewiring of Biological Networks

2011
PLoS Comput Biol
PMCID: 3017101
PMID: 21253555
DOI: 10.1371/journal.pcbi.1001050

[…] re constructed in two steps. We first obtained phosphorylation sites identified by MassSpec , and also obtained kinase binding specificity data from kinase binding specificity experiments ; then used MOTIPS analysis pipeline to identify responsible kinases for each phosphorylation site by matching position weight matrices (PWMs) . Structural Interaction Networks (SINs) for H. sapiens and S. cerevi […]

call_split

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

2009
PLoS Biol
PMCID: 2756588
PMID: 19841731
DOI: 10.1371/journal.pbio.1000218
call_split See protocol

[…] e, and hence added pseudocounts. We scaled the number of pseudocounts added by the entropy of each position . Each matrix was used to scan the yeast proteome to identify the best matches. We used the MOTIPS analysis pipeline to identify possible binders for each domain. Only the proteome-scanning module of the pipeline was utilized, which performs a highly optimized search in the yeast proteome fo […]


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MOTIPS institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA

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