Post-Translational Modification site Prediction - User Interface

Introduction

By covalently attaching to individual amino acids various functional molecules such as phosphates, lipids, or proteins, post-translational modifications (PTMs) alter a proteiní»s biochemical nature significantly, and play essential roles in a wide variety of cellular processes. Although more than 350 types of PTMs have been discovered (see the database of protein translational modifications at http://abrf.org/index.cfm/dm.home), only a few of them have been well-characterized (please refer to the following list of PTM prediction servers). Experimental identification of proteinsí» PTM sites is labor-intensive and usually limited by the availability of enzymatic reactions. In silico prediction could be a promising strategy to conduct preliminary analyses and greatly reduce the number of potential targets that need further in vivo or in vitro confirmation.

Since the diversity in the user interface of different prediction servers could greatly hinder experimental biologists in using these servers, we propose to develop a protocol of a unified user interface (UI) for in silico prediction servers for proteinsí» PTMs, based on our own work and other groupsí» work on PTM site prediction. Computational biologists may follow this protocol to provide a uniform user interface, regardless of the PTM types and the computation algorithms. And wet lab biologists would be able to use any PTM site prediction servers compliant to this protocol after getting familiar with one of them.

Reference

A general user interface for prediction servers of proteins' post-translational modification sites.
Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu.
Nature Protocols 1 (3): 1318-1321.


An updated list of almost all the available PTM prediction servers (2006-07-31)

Please contact the authors of this protocol for adding your PTM site prediction servers to this list.

General PTM
  ELM http://elm.eu.org/
  ProSite http://www.expasy.org/prosite/
  AutoMotif http://automotif.bioinfo.pl/

Phosphorylation
  GPS http://csbl.bmb.uga.edu/~ffzhou/gps_web/
  DisPhos http://core.ist.temple.edu/pred/pred.html
  ScanSite http://scansite.mit.edu/
  KinasePhos http://kinasephos.mbc.nctu.edu.tw/
  NetPhos http://www.cbs.dtu.dk/services/NetPhos/
  NetPhosK http://www.cbs.dtu.dk/services/NetPhosK/
  PPSP http://bioinformatics.lcd-ustc.org/PPSP/

Glycosylation
  DictyOGlyc http://www.cbs.dtu.dk/services/DictyOGlyc/
  NetGlycate http://www.cbs.dtu.dk/services/NetGlycate/
  NetNGlyc http://www.cbs.dtu.dk/services/NetNGlyc/
  NetOGlyc http://www.cbs.dtu.dk/services/NetOGlyc/
  YinOYang http://www.cbs.dtu.dk/services/YinOYang/
  GPI http://mendel.imp.ac.at/gpi/gpi_server.html
  DGPI http://129.194.185.165/dgpi/DGPI_demo_en.html
  GPI-SOM http://gpi.unibe.ch/
  GlycoSee http://dbptm.mbc.nctu.edu.tw/GlycoSee/
  Glyprot http://www.glycosciences.de/modeling/glyprot/php/main.php

Sumoylation
  SUMOsp http://csbl.bmb.uga.edu/~ffzhou/sumosp/
  SUMOplot http://www.abgent.com/doc/sumoplot

Palmitoylation
  CSS-Palm http://csbl.bmb.uga.edu/~ffzhou/css_palm/
  NBA-Palm http://www.bioinfo.tsinghua.edu.cn/~tigerchen/NBA-Palm/

Acetylation
  NetAcet http://www.cbs.dtu.dk/services/NetAcet/

Sulfation
  Sulfinator http://www.expasy.org/tools/sulfinator/
  SulfoSite http://sulfosite.mbc.nctu.edu.tw/

Myristoylation
  Myristoylator http://www.expasy.org/tools/myristoylator/
  NMT http://mendel.imp.ac.at/myristate/SUPLpredictor.htm

Prenylation
  PrePS http://mendel.imp.ac.at/sat/PrePS/index.html

Methylation
  MeMo http://www.bioinfo.tsinghua.edu.cn/~tigerchen/memo.html
  PMP http://156.56.92.123/methylation/index.php


Computational Systems Biology Laboratory,
Department of Biochemical and Molecular Biology and Institute of Bioinformatics,
University of Georgia, Athens, GA 30602, USA

Laboratory of Cellular Dynamics,
Hefei National Laboratory for Physical Sciences,
and the University of Science and Technology of China, Hefei, China 230027

Last update: 2007-04-06