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Priyanshu Kumar
Under reviewComputers in Biology and Medicine · First author

Structural and regulatory effects of EGFR variants in glioblastoma

Computational study of coding and non-coding EGFR variants

Code

Overview

Coding and non-coding EGFR variants assessed with consensus pathogenicity prediction, structural modeling, docking, molecular dynamics, and chromatin-context analysis.

The analyses cover variant annotation and prioritization, protein structure, molecular docking and dynamics of wild-type and variant EGFR, regulatory predictions, and TCGA expression and clinical associations.

Pathogenicity predictors · HADDOCK3 · AutoDock Vina · GROMACS · AlphaGenome · Enformer

Variant sources
NCBI dbSNP (coding) · COSMIC v103 (non-coding)
Simulated systems
Wild-type, V774M, and L861Q EGFR
Docking partners
Cetuximab, nimotuzumab, erlotinib
Authors
Kumar P, Singh G, Kaur S, Sharma P

Figures

Workflow diagram from SNP retrieval through functional pathogenicity predictors to structural analyses including docking and molecular dynamics.
Fig. 1. Overview of variant retrieval, functional annotation, and structural analyses.