PEIMAN – Enrichment Analysis in Post Translational Modification (PTM) types

PEIMAN 1.0

:: DESCRIPTION

PEIMAN (Post translational modification, Enrichment, Integration and Matching ANalysis ) is a standalone software for enrichment analysis in post translational modification (PTM) types. The software also provides the comparison between two different lists of proteins, focusing on PTM types. Investigating the PTM frequency in each list is also available.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 PEIMAN

:: MORE INFORMATION

Citation

PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis.
Nickchi P, Jafari M, Kalantari S.
Database (Oxford). 2015 Apr 23;2015. pii: bav037. doi: 10.1093/database/bav037.

Forcefield_PTM – AMBER Forcefield Parameters for Post-translational Modifications

Forcefield_PTM

:: DESCRIPTION

Forcefield_PTM is a set of self-consistent AMBER forcefield parameters for frequently occurring post-translational modifications (PTMs).

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications.
Khoury GA, Thompson JP, Smadbeck J, Kieslich CA, Floudas CA.
J Chem Theory Comput. 2013 Dec 10;9(12):5653-5674.

PhosphOrtholog – Cross-species Mapping of Orthologous Protein Post-translational Modification

PhosphOrtholog

:: DESCRIPTION

PhosphOrtholog is a tool to map post-translational modification sites on proteins orthologous across species

::DEVELOPER

PhosphOrtholog team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.
Chaudhuri R, Sadrieh A, Hoffman NJ, Parker BL, Humphrey SJ, St?ckli J, Hill AP, James DE, Yang JY.
BMC Genomics. 2015 Aug 19;16(1):617. doi: 10.1186/s12864-015-1820-x.

MassShiftFinder 1.09 – Blind search for Post-translational Modifications and Amino Acid Substitutions

MassShiftFinder 1.09

:: DESCRIPTION

MassShiftFinder is a software tool for doing blind search using peptide mass fingerprints from two proteases with different cleavage specificities. The algorithm relies on overlapping peptides for the two proteases used, and can indicate both modifications and amino acid substitutions. The method can help restrict the area where the modification has occurred.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 MassShiftFinder

:: MORE INFORMATION

Citation

BMC Res Notes. 2008 Dec 19;1:130.
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.
Barsnes H, Mikalsen SO, Eidhammer I.

dbPTM 3.0 – Information Repository of Protein Post-translational Modification

dbPTM 3.0

:: DESCRIPTION

dbPTM is an informative resource for protein post-translational modifications (PTMs).

::DEVELOPER

dbPTM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D622-7.
dbPTM: an information repository of protein post-translational modification.
Lee TY, Huang HD, Hung JH, Huang HY, Yang YS, Wang TH.

AMS 4.0-1.5 – Consensus Prediction of Post-translational Modifications in Protein Sequences

AMS 4.0-1.5

:: DESCRIPTION

AMS (AutoMotif Service) predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences.

::DEVELOPER

AMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 AMS

:: MORE INFORMATION

Citation

Amino Acids. 2012 Aug;43(2):573-82. doi: 10.1007/s00726-012-1290-2.
AMS 4.0: consensus prediction of post-translational modifications in protein sequences.
Plewczynski D, Basu S, Saha I.

PTMClust 1.1 – A Post-translational Modification Refinement Algorithm

PTMClust 1.1

:: DESCRIPTION

PTMClust is a software that can be applied to the output of blind PTM (Post-translational Modification) search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We showed that our technique outperforms two standard clustering algorithms on a simulated dataset. Additionally, we showed that our algorithm significantly improves sensitivity and specificity when applied to the output of three different blind PTM search engines, SIMS, InsPecT and MODmap. Additionally, PTMClust markedly outforms another PTM refinement algorithm, PTMFinder. We demonstrate that our technique is able to reduce false PTM assignments, improve overall detection coverage and facilitate novel PTM discovery, including terminus modifications. We applied our technique to a large-scale yeast MS/MS proteome profiling dataset and found numerous known and novel PTMs. Accurately identifying modifications in protein sequences is a critical first step for PTM profiling, and thus our approach may benefit routine proteomic analysis.

::DEVELOPER

Frey Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MatLab

:: DOWNLOAD

  PTMClust

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Mar 15;27(6):797-806. Epub 2011 Jan 22.
Computational refinement of post-translational modifications predicted from tandem mass spectrometry.
Chung C, Liu J, Emili A, Frey BJ.