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Welcome to the Post Translational Modification Structural Database (PTM-SD). Proteins are composed of a succession of amino acid residues. Their 3D structures are the support of major crucial biological functions. Post translational modifications (PTMs) are covalent chemical modifications of proteins that typically occur after the protein synthesis. They allow a fine and sometimes obligatory modulation of biological functions; they can determine proteins activity state, localization, turnover, and interactions with other proteins. PTM-SD provides an access to proteins for which PTMs are both experimentally annotated and structurally resolved. We have used different databases to characterize the different PTMs resolved in the protein structures (see HELP page and the FLOWCHART for details on the difficulty to define them properly): Protein structures are found in Protein Data Bank (http://www.rcsb.org/pdb/home/home.do) [ref] Sequences contained in PDB were compared with sequences of UniProt database (http://www.uniprot.org/) [ref] PTMs found in the protein structures were compared with PTMs annotated in dbPTM (http://dbptm.mbc.nctu.edu.tw/) [ref] and PTMCuration (http://selene.princeton.edu/PTMCuration/) [ref] |
Compute pie chart of organism distribution, protein distribution and PTM annotation distribution. (Read more...) |
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Compute local structure entropy at the surrounding positions of PTM sites. (Read more...) |
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Compute dendogram and histogram of pairwise sequence identity of selected proteins. (Read more...) |
Pierrick Craveur |
Joseph Rebehmed |
Alexandre G. de Brevern |
This webserver has been designed by Pierrick Craveur, Joseph Rebehmed and Alexandre G. de Brevern.
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You can also look at other tools developed by our team : |
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[ VLDPws ] (Esque, Leonard, de Brevern and Oguey, Nucleic Acid Res, 2013). [ mulPBA ] (Leonard, Jospeh, Srinivasan, Gelly et de Brevern, J Biol Struct Dyn, 2013). [ PredyFlexy ] (de Brevern, Bornot, Craveur, Etchebest and Gelly, Nucleic Acid Res , 2012). [ iPBA ] (Gelly, Joseph, Srinivasan et de Brevern., Nucleic Acid Res , 2011). [ Protein Peeling 3D ] (Gelly and de Brevern, Bioinformatics , 2011). [ LocPred ] (de Brevern et al., In Silico Biology , 2004). |
Databases related to Post-Translational Modifications: | More general databases : |
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PTMcode: https://ptmcode.embl.de/ dbPTM: https://dbptm.mbc.nctu.edu.tw/ PTM Statistics Curator: https://selene.princeton.edu/PTMCuration/ PHOSIDA : https://www.phosida.com/ PHOSPHOSITE: https://www.phosphosite.org/homeAction.do PHOSPHOelm: https://phospho.elm.eu.org/ OglycBase: https://www.cbs.dtu.dk/databases/OGLYCBASE/ | PDB : https://www.rcsb.org/pdb/home/home.do uniprot : https://www.uniprot.org/ HPRD: https://www.hprd.org/ |