Computational Methods for Predicting Post-Translational Modification Sites

lt;p>1.              Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling

Anthony A. Iannetta and Leslie M. Hicks

2.     PLDMS: Phosphopeptide Library Dephosphorylation followed by Mass Spectrometry Analysis to Determine the Specificity of Phosphatases for Dephosphorylation Site Sequences

Thomas Kokot, Bernhard Hoermann, Dominic Helm, Jeremy E. Chojnacki, Mikhail M. Savitski, and Maja Köhn

3.              FEPS: A tool for Feature Extraction from Protein Sequence

Hamid Ismail, Clarence White, Hussam AL-barakati, Robert H. Newman, and Dukka B. KC

4.              A pre-trained ELECTRA model for Kinase-specific Phosphorylation Site Prediction

Lei Jiang, Duolin Wang, and Dong Xu

5.              iProtGly-SS: A Tool to Accurately Predict Protein Glycation Site Using structural-based Features

Abdollah Dehzangi, Alok Sharma, and Swakkhar Shatabda

6.              Functions of Glycosylation and Related Web Resources for its Prediction

Kiyoko F. Aoki-Kinoshita

7.              Analysis of Post-Translational Modifications in Arabidopsis Proteins and Metabolic Pathways using the FAT-PTM Database

8.              Bioinformatic Analyses of Peroxiredoxins and RF-Prx: A RANDOM FOREST-BASED PREDICTOR and classifier for Prxs

Hussam AL-barakati, Robert H. Newman, Dukka B. KC, and Leslie B. Poole

9.              Computational prediction of N- and O-linked glycosylation sites for human and mouse proteins

Ghazaleh Taherzadeh, Matthew Campbell, and Yaoqi Zhou 

10.           iPTMnet RESTful API for Post-Translational Modification Network Analysis

Sachin Gavali, Karen E. Ross, Julie Cowart, Chuming Chen, and Cathy H. Wu

11.           Systematic Characterization of Lysine Post-Translational Modification Sites using MUscADEL

Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana Marquez-Lago, André Leier, Geoffrey I. Webb, Dakang Xu, Tatsuya Akutsu, and Jiangning Song

Nolan English and Matthew Torres

13.           Exploration of Protein Post-Translational Modification Landscape and Crosstalk with CrossTalkMapper

Arthur Grimaud, Frederik Holck, Louise Marie Buur, Rebecca Kirsch, and Veit Schwämmle

14.           PTM-X: Prediction of Post-Translational Modification Crosstalk Within and Across Proteins

Yuxuan Li,Yuanhua Huang, and Tingting Li

15.           Deep Learning-Based Advances In Protein Post-Translational Modification Site And Protein Cleavage Prediction

Subash C. Pakhrin, Suresh Pokharel, Hiroto Saigo, and Dukka B. KC