Post-Translational Modification Prediction & Pathway Impact — Hands-on

Go from PTM site prediction to systems-level interpretation. Learn robust PTM site predictors, kinase/substrate inference, enrichment methods, and pathway impact analyses to convert raw PTM calls into clear, defensible biological mechanisms—with automated, reproducible reports.

Post-Translational Modification Prediction & Pathway Impact

Help Desk · WhatsApp

Session Index

Session 1 — PTM Landscape & Site Prediction Session 2 — Kinases, Motifs & Network Context Session 3 — PTM Enrichment & Pathway Impact Session 4 — Mini Capstone: PTM Signature → Mechanism

Session 1

Fee: Rs 6300

PTM Landscape & Site Prediction

PTM types & biology: phosphorylation, glycosylation, ubiquitination, acetylation, methylation

Theory

Sequence- and structure-based site prediction (overview & practice)

NetPhos/MusiteDeep GPS/KinasePhos NetOGlyc/NetNGlyc UbPred/BDM-PUB

Confidence scoring, calibration & negatives

ROC/PR threshold tuning cross-validation

Session 2

Fee: Rs 8400

Kinases, Motifs & Network Context

Kinase–substrate mapping & motif models; evidence curation

PhosphoSitePlus ELM/PROSITE motif-x

PPI & pathway overlays for PTM context

STRING/Cytoscape Reactome/KEGG topology features

Structural proximity & accessibility of sites (optional)

SASA/contacts disorder/linkers

Session 3

Fee: Rs 11200

PTM Enrichment & Pathway Impact

PTM set enrichment: PTM-SEA/KSEA & kinase activity inference

PTM-SEA KSEA/KEA3 rank-based/preranked

From sites to pathways: scoring nodes/edges with PTM evidence

Reactome/GO/KEGG network propagation causal graphs*

QC, multiple testing & effect-size reporting

FDR control NES/ES

Session 4

Fee: Rs 14000

Mini Capstone: PTM Signature → Mechanism

From predicted/observed PTM sites to implicated kinases and pathways; build a narrative

Theory + Practical

Provenance & reproducibility: configs, databases, versions & logs

YAML/JSON configs Snakemake/Nextflow Quarto summary

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

Post-Translational Modification Prediction & Pathway Impact Training | Kinase Maps, PTM-SEA/KSEA & Pathways

Post-Translational Modification Prediction & Pathway Impact — Hands-on