Tag: PTM

Specialize 1.0 – Identification of Peptides with complex PTM from Tandem Mass Spectra

Specialize 1.0

:: DESCRIPTION

Specialize is a novel approach to enable the expedited development of new algorithms for any types of PTM (post-translational modifications) peptide fragmentation.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Specialize

:: MORE INFORMATION

Citation

A Turn-key Approach for Large-scale Identification of Complex Post-translational Modifications
Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. J
Proteome Res. 2014 Mar 7;13(3):1190-9. doi: 10.1021/pr400368u. Epub 2014 Jan 29.

PCTpred – PTM Cross-Talk predictor

PCTpred

:: DESCRIPTION

PCTpred is a computational method that can accurately identify PTM cross-talk pairs in a given protein sequence or structure.

::DEVELOPER

Rong Liu’s Lab of Protein Bioinformatics at Huazhong Agriculture University!

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl
:: DOWNLOAD

PCTpred

:: MORE INFORMATION

Citation:

Brief Bioinform 2019 Jan 11
Structure-based Prediction of Post-Translational Modification Cross-Talk Within Proteins Using Complementary Residue- And Residue Pair-Based Features
Hui-Fang Liu 1, Rong Liu 1

Luciphor2 – PTM-site localization on MS/MS data

Luciphor2

:: DESCRIPTION

Luciphor2 is a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Luciphor2

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.
Fermin D, Avtonomov D, Choi H, Nesvizhskii AI

PTMcode 2 – Known and predicted PTM Functional Associations

PTMcode 2

:: DESCRIPTION

PTMcode is a web resource for known and predicted functional associations between protein post-translational modifications (PTMs) within and between proteins.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P.
Nucleic Acids Res. 2015 Jan;43(Database issue):D494-502. doi: 10.1093/nar/gku1081