PTM Related Resources

PTM : Meta        Type : Database

CPLM
Resource Type : DB
Description :
CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs). The CPLM database was extended and adapted from our CPLA 1.0 (Compendium of Protein Lysine Acetylation) database (Liu et al., 2011), and the 2.0 release contain ...
Taxonomy : N/A
Visit : http://cplm.biocuckoo.org/

Publication Information

Article : CPLM: a database of protein lysine modifications.
Author : Zexian Liu, Yongbo Wang, Tianshun Gao, Zhicheng Pan, Han Cheng, Qing Yang, Zhongyi Cheng2, Anyuan Guo, Jian Ren and Yu Xue
Years : 2014
PubMed : 24214993

CrosstalkDB
Resource Type : DB
Description :
This database aims to collect mass spectrometry data of multiply modified histones or histone tails. You can search, analyze and download data from this database without having to log in. Quantification can be based on either spectral counting or peak intensities. We recommend isoScale and Histon ...
Taxonomy : N/A
Visit : http://crosstalkdb.bmb.sdu.dk/

Publication Information

Article : Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk
Author : Veit Schwammle, Claudia-Maria Aspalter, Simone Sidoli,and Ole N. Jensen
Years : 2014
PubMed : 24741113

dbPTM
Resource Type : DB
Description :
Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high-throughput of mass spectrometry-based methods in identifying site-specifi ...
Taxonomy : N/A
Visit : http://dbptm.mbc.nctu.edu.tw/index.php

Publication Information

Article : DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
Author : Cheng-Tsung Lu, Kai-Yao Huang, Min-Gang Su, Tzong-Yi Lee, Neil Arvin Bretana, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen and Hsien-Da Huang
Years : 2013
PubMed : 23193290

HIstome
Resource Type : DB
Description :
Post-translational modification (PTM) of histones is a crucial step in epigenetic regulation of a gene. N-terminal tails of histones are the most accessible regions of these peptide as they protrude from the nucleosome and possess no specific structure. These tails are subjected to various modificat ...
Taxonomy : Eukaryota, Animals
Visit : http://www.actrec.gov.in/histome/ptm_main.php

Publication Information

Article : HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes.
Author : Satyajeet P. Khare, Farhat Habib, Rahul Sharma, Nikhil Gadewal, Sanjay Gupta and Sanjeev Galande
Years : 2012
PubMed : 22140112

novPTMenzy
Resource Type : DB
Description :
Several attempts have been made to catalog the wealth of available information on Post-Translational Modification(PTMs) for easy retrieval and analysis. However, the tools and databases available mainly focus on modified sites or enzymes of well-known PTMs. Tools for newly discovered PTMs like AMPyl ...
Taxonomy : N/A
Visit : http://www.nii.ac.in/novptmenzy.html

Publication Information

Article : novPTMenzy: a database for enzymes involved in novel post-translational modifications.
Author : Shradha Khater and Debasisa Mohanty
Years : 2015
PubMed : 25931459

ProteomeScout
Resource Type : DB
Description :
ProteomeScout is a database of proteins and post-translational modifications. There are two main data types in ProteomeScout. 1) Proteins: Visualize proteins or annotate your own proteins. 2) Experiments: You can load a new experiment or browse and analyze an existing experiment. ...
Taxonomy : N/A
Visit : https://proteomescout.wustl.edu/

Publication Information

Article : ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.
Author : Matthew K. Matlock, Alex S. Holehouse and Kristen M. Naegle
Years : 2015
PubMed : 25414335

PSP
Resource Type : DB
Description :
PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation. See About PhosphoSite above for more information. Please ...
Taxonomy : Eukaryota, Animals
Visit : http://www.phosphosite.org/homeAction.do

Publication Information

Article : PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.
Author : Peter V. Hornbeck, Bin Zhang, Beth Murray, Jon M. Kornhauser, Vaughan Latham and Elzbieta Skrzypek
Years : 2015
PubMed : 25514926

PTMCode
Resource Type : DB
Description :
PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins. It currently contains 316,546 modified sites from 69 different PTM types which are also propagated through ortholgs between 19 differe ...
Taxonomy : Eukaryota
Visit : http://ptmcode.embl.de/

Publication Information

Article : PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins
Author : Pablo Minguez, Ivica Letunic, Luca Parca1, Luz Garcia-Alonso, Joaquin Dopazo,Jaime Huerta-Cepas and Peer Bork1
Years : 2014
PubMed : 25361965

PTMfunc
Resource Type : DB
Description :
PTMfunc is a repository of functional predictions for protein post-translational modifications (PTMs). To find predictions for your protein of interest just search using a protein name or ID in the search box above. We rely mostly on ids from ENSEMBL but also have protein names for most species. For ...
Taxonomy : N/A
Visit : http://ptmfunc.com/

Publication Information

Article : Systematic functional prioritization of protein posttranslational modifications.
Author : Pedro Beltrao , Véronique Albanèse, Lillian R. Kenner, Danielle L. Swaney, Alma Burlingame, Judit Villén, Wendell A. Lim, James S. Fraser, Judith Frydman, Nevan J. Krogan
Years : 2012
PubMed : 22817900

PTM-SD
Resource Type : DB
Description :
Posttranslational modifications (PTMs) define covalent and chemical modifications of protein residues. They play important roles in modulating various biological functions. Current PTM databases contain important sequence annotations but do not provide informative 3D structural resource about these ...
Taxonomy : N/A
Visit : http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD/

Publication Information

Article : PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.
Author : Pierrick Craveur, Joseph Rebehmed and Alexandre G. de Brevern
Years : 2014
PubMed : 24857970

RedoxDB
Resource Type : DB
Description :
SUMMARY: Redox regulation and signaling, which are involved in various cellular processes, have become one of the research focuses in the past decade. Cysteine thiol groups are particularly susceptible to post-translational modification, and their reversible oxidation is of critical role in redox re ...
Taxonomy : N/A
Visit : http://biocomputer.bio.cuhk.edu.hk/RedoxDB/

Publication Information

Article : RedoxDB--a curated database for experimentally verified protein oxidative modification.
Author : Ming-an Sun, Yejun Wang, Han Cheng, Qing Zhang, Wei Ge and Dianjing Guo
Years : 2012
PubMed : 22833525

RESID
Resource Type : DB
Description :
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. ...
Taxonomy : N/A
Visit : http://pir.georgetown.edu/resid/

Publication Information

Article : The RESID Database of Protein Modifications: 2003 developments.
Author : John S. Garavelli
Years : 2003
PubMed : 12520062

SysPTM
Resource Type : DB
Description :
SysPTM Version 2.0, updated June 15th, 2013. Visits: 110. SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools. ...
Taxonomy : N/A
Visit : http://lifecenter.sgst.cn/SysPTM/

Publication Information

Article : SysPTM 2.0: an updated systematic resource for post-translational modification.
Author : Jing Li, Jia Jia, Hong Li, Jian Yu, Han Sun, Ying He, Daqing Lv, Xiaojuan Yan2, Michael O. Glocker, Liangxiao Ma, Jiabei Yang, Ling Li, Wei Li, Guoqing Zhang, Qian Liu, Yixue Li and Lu Xie
Years : 2014
PubMed : 24705204

topPTM
Resource Type : DB
Description :
topPTM is a database that integrates experimentally verified post-translational modifications (PTMs) from available databases and research articles, and annotates the PTM sites on transmembrane proteins with structural topology. The biological effects of PTMs on transmembrane proteins include phosph ...
Taxonomy : N/A
Visit : http://topptm.cse.yzu.edu.tw/

Publication Information

Article : topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.
Author : Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang and Tzong-Yi Lee
Years : 2014
PubMed : 24302577