Editing Post-translational modification (section)

== Databases and tools ==

[[File:Image for Wiki 2.jpg|alt=|thumb|Flowchart of the process and the data sources to predict PTMs.<ref name="ReferenceA">{{cite journal | vauthors = Lee TY, Huang HD, Hung JH, Huang HY, Yang YS, Wang TH | title = dbPTM: an information repository of protein post-translational modification | journal = Nucleic Acids Research | volume = 34 | issue = Database issue | pages = D622-7 | date = January 2006 | pmid = 16381945 | pmc = 1347446 | doi = 10.1093/nar/gkj083 }}</ref>  |440x440px]]

Protein sequences contain sequence motifs that are recognized by modifying enzymes, and which can be documented or predicted in PTM databases. With the large number of different modifications being discovered, there is a need to document this sort of information in databases. PTM information can be collected through experimental means or predicted from high-quality, manually curated data. Numerous databases have been created, often with a focus on certain taxonomic groups (e.g. human proteins) or other features.

=== List of resources ===
* [http://www.phosphosite.org/ PhosphoSitePlus]<ref>{{cite journal | vauthors = Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E | title = PhosphoSitePlus, 2014: mutations, PTMs and recalibrations | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D512-20 | date = January 2015 | pmid = 25514926 | pmc = 4383998 | doi = 10.1093/nar/gku1267 }}</ref> – A database of comprehensive information and tools for the study of mammalian protein post-translational modification
* [[ProteomeScout]]<ref name="ReferenceB">{{cite journal | vauthors = Goel R, Harsha HC, Pandey A, Prasad TS | title = Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis | journal = Molecular BioSystems | volume = 8 | issue = 2 | pages = 453–63 | date = February 2012 | pmid = 22159132 | pmc = 3804167 | doi = 10.1039/c1mb05340j }}</ref> – A database of proteins and post-translational modifications experimentally
* [[Human Protein Reference Database]]<ref name="ReferenceB"/> – A database for different modifications and understand different proteins, their class, and function/process related to disease causing proteins
* [[PROSITE]]<ref>{{cite journal | vauthors = Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N | title = PROSITE, a protein domain database for functional characterization and annotation | journal = Nucleic Acids Research | volume = 38 | issue = Database issue | pages = D161-6 | date = January 2010 | pmid = 19858104 | pmc = 2808866 | doi = 10.1093/nar/gkp885 }}</ref> – A database of Consensus patterns for many types of PTM's including sites
* [[Protein Information Resource|RESID]]<ref>{{cite journal | vauthors = Garavelli JS | title = The RESID Database of Protein Modifications: 2003 developments | journal = Nucleic Acids Research | volume = 31 | issue = 1 | pages = 499–501 | date = January 2003 | pmid = 12520062 | pmc = 165485 | doi = 10.1093/nar/gkg038 }}</ref> – A database consisting of a collection of annotations and structures for PTMs.
* [https://research.bioinformatics.udel.edu/iptmnet/ iPTMnet] <ref>{{cite journal | vauthors = Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH | title = iPTMnet: an integrated resource for protein post-translational modification network discovery | journal = Nucleic Acids Research | volume = 46 | issue = 1 | pages = D542–D550 | date = January 2018 | pmid = 2914561 | pmc = 5753337 | doi = 10.1093/nar/gkx1104}}</ref>– A database that integrates PTM information from several knowledgbases and text mining results. 
* [[dbPTM]]<ref name="ReferenceA"/> – A database that shows different PTM's and information regarding their chemical components/structures and a frequency for amino acid modified site
* [https://www.uniprot.org/help/post-translational_modification Uniprot] has PTM information although that may be less comprehensive than in more specialized databases.[[File:Image for Wiki 1.jpg|alt=|thumb|Effect of PTMs on protein function and physiological processes.<ref>{{cite journal | vauthors = Audagnotto M, Dal Peraro M | title = In silico prediction tools and molecular modeling | journal = Computational and Structural Biotechnology Journal | volume = 15 | pages = 307–319 | date = 2017-03-31 | pmid = 28458782 | pmc = 5397102 | doi = 10.1016/j.csbj.2017.03.004 }}</ref>|440x440px]]
* [https://www.oglcnac.mcw.edu/ The ''O''-GlcNAc Database]<ref>{{cite journal | vauthors = Wulff-Fuentes E, Berendt RR, Massman L, Danner L, Malard F, Vora J, Kahsay R, Olivier-Van Stichelen S | title = The human ''O''-GlcNAcome database and meta-analysis | journal = Scientific Data | volume = 8 | date = January 2021 | issue = 1 | page = 25 | pmid = 33479245 | pmc = 7820439 | doi = 10.1038/s41597-021-00810-4 | bibcode = 2021NatSD...8...25W }}</ref><ref>{{cite journal | vauthors = Malard F, Wulff-Fuentes E, Berendt RR, Didier G, Olivier-Van Stichelen S | title = Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database | journal = Database (Oxford) | volume = 2021 | date = July 2021 | page = 1 | pmid = 34279596 | doi = 10.1093/database/baab039 | pmc = 8288053 }}</ref> - A curated database for protein O-GlcNAcylation and referencing more than 14 000 protein entries and 10 000 ''O''-GlcNAc sites.

=== Tools ===
List of software for visualization of proteins and their PTMs
* [[PyMOL]]<ref>{{cite journal | vauthors = Warnecke A, Sandalova T, Achour A, Harris RA | title = PyTMs: a useful PyMOL plugin for modeling common post-translational modifications | journal = BMC Bioinformatics | volume = 15 | issue = 1 | pages = 370 | date = November 2014 | pmid = 25431162 | pmc = 4256751 | doi = 10.1186/s12859-014-0370-6 | doi-access = free }}</ref> – introduce a set of common PTM's into protein models
* [[AWESOME]]<ref>{{cite journal | vauthors = Yang Y, Peng X, Ying P, Tian J, Li J, Ke J, Zhu Y, Gong Y, Zou D, Yang N, Wang X, Mei S, Zhong R, Gong J, Chang J, Miao X | title = AWESOME: a database of SNPs that affect protein post-translational modifications | journal = Nucleic Acids Research | volume = 47 | issue = D1 | pages = D874–D880 | date = January 2019 | pmid = 30215764 | pmc = 6324025 | doi = 10.1093/nar/gky821 }}</ref> – Interactive tool to see the role of single nucleotide polymorphisms to PTM's
* [[UCSF Chimera|Chimera]]<ref>{{cite journal | vauthors = Morris JH, Huang CC, Babbitt PC, Ferrin TE | title = structureViz: linking Cytoscape and UCSF Chimera | journal = Bioinformatics | volume = 23 | issue = 17 | pages = 2345–7 | date = September 2007 | pmid = 17623706 | doi = 10.1093/bioinformatics/btm329 | doi-access = free }}</ref> – Interactive Database to visualize molecules