PyTMs statistics

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Citations per year

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

This map represents all the scientific publications referring to PyTMs per scientific context
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Associated diseases

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Popular tool citations

chevron_left Phosphorylation site prediction Acetylation site prediction Methylation site prediction Hydroxylation site prediction chevron_right
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Protocols

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

Versioning


No version available

Publication for PyTMs

PyTMs citations

 (4)
call_split

SIRT2 deacetylase regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation

2018
eLife
PMCID: 5860870
PMID: 29504933
DOI: 10.7554/eLife.32952.020
call_split See protocol

[…] Models 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 we […]

call_split

Phosphorylation of the phytosulfokine peptide receptor PSKR1 controls receptor activity

2017
J Exp Bot
PMCID: 5441923
PMID: 28338789
DOI: 10.1093/jxb/erx030
call_split See protocol

[…] h 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 . […]

library_books

Structural insights into the recognition of phosphorylated FUNDC1 by LC3B in mitophagy

2016
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 as ac […]

library_books

Proteomic analysis reveals diverse proline hydroxylation mediated oxygen sensing cellular pathways in cancer cells

2016
Oncotarget
PMCID: 5346705
PMID: 27764789
DOI: 10.18632/oncotarget.12632

[…] anually 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 []. […]


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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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