PyTMs statistics

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chevron_left Phosphorylation site prediction Acetylation site prediction Methylation site prediction Hydroxylation site prediction chevron_right
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PyTMs specifications

Information


Unique identifier OMICS_06774
Name PyTMs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PyTMs

PyTMs in publications

 (4)
PMCID: 5860870
PMID: 29504933
DOI: 10.7554/eLife.32952.020

[…] of gsk3β protein were generated from the crystal structure (pdb id 4nm0 a). computer aided acetylated lysine (ack183) mutant was generated over the crystal structure (pdb id 4nm0 a), using the pytms plugin of pymol (). ucsf chimera software package was used for visualization and generation of the final images ()., md simulations on the initial models of gsk3β wild-type and acetylated gsk3β […]

PMCID: 5441923
PMID: 28338789
DOI: 10.1093/jxb/erx030

[…] as the n-lobe, was done based on the model of bri1 generated by . secondary structures were named according to . phosphorylations at specific residues in the model were added using the pymol plugin pytms by ., statistical analysis of in vitro kinase activities was carried out with r (https://cran.r-project.org/doc/faq/r-faq.html). for all pairwise comparisons, a kruskal–wallis test […]

PMCID: 5233613
PMID: 27757847
DOI: 10.1007/s13238-016-0328-8

[…] round of the docking procedure was performed as follows. first, coordinates of the missing residues of the fundc1 peptide were built using pymol and ser17 in the fundc1 peptide was phosphorylated by pytms (warnecke et al., ). then, inputs of the haddock webserver were extracted from the crystal structures. interface residues involved in inter-chain hydrogen bonding interactions were treated […]

PMCID: 5346705
PMID: 27764789
DOI: 10.18632/oncotarget.12632

[…] curated from the pdb data deposited in the uniprot database []. individual protein structures were visualized by pymol (the pymol molecular graphics system, version 1.8 schrödinger, llc) with pytms plugin []., synthetic peptides were acquired from gl biochem ltd (shanghai, china). the peptides were reconstituted with hplc buffer a and analyzed by proxeon nanolc-orbitrap fusion mass […]


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PyTMs institution(s)
Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Applied Immunology and Immunotherapy, Karolinska Hospital, Stockholm, Sweden; Department of Medicine Solna, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden

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