Pathmanaban Ramasamy

Scop3P-Toolkit provides an open-source framework for integrating PTMs, mutations, and proteomics data with structural and functional annotations to enable reproducible analysis.

InstaNovo-P improves phosphorylated peptide detection and site localization in phosphoproteomics by using a transformer-based model fine-tuned on phosphoproteomics data.

Scop3P is updated to integrate phosphorylation sites with structural, functional, and mutational data, enhancing phosphosite interpretation and disease context.

The paper evaluates AlphaFold models' ability to predict phosphorylation-induced structural changes in proteins using experimentally derived conformational ensembles.

The paper develops a targeted LC-MS method to quantify SARS-CoV-2 spike protein expression and enables proteome profiling of infected cells.

This study evaluates PTM predictors using protein language models, revealing a training bias from proteomics data that overestimates prediction accuracy and suggests a solution through negative sample filtering.

The paper analyzes phospho-proteomics data to characterize phosphorylation sites, showing phosphorylated residues are more flexible and disease-linked mutations in rigid regions are more prevalent.

The paper develops SECRiFY, a method to assess secretability of protein fragments in yeast, revealing intrinsic disorder and flexibility as key factors.

Scop3P provides a comprehensive database of human phosphosites with structural and biophysical context, integrating sequence, structure, and phosphoproteomics data.