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Protocol for predicting γ-tocotrienol and δ-tocotrienol binding to colorectal cancer-related proteins using
Ali Qusay Khalid1, Saatheeyavaane Bhuvanendran1, Kasthuri Bai Magalingam1
1Food as Medicine Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Malaysia.
Abstract:
We present a protocol for predicting γ-tocotrienol (γT3) and δ-tocotrienol (δT3) binding to colorectal cancer-related proteins using Schrödinger's Maestro and Glide. The protocol describes protein preparation, ligand processing, and receptor grid generation, followed by docking simulations. It outputs binding affinities (kcal/mol) and interaction maps, with δT3 expected to bind slightly more strongly. This workflow includes checkpoints and troubleshooting, providing a reproducible framework suitable for users with intermediate to advanced molecular modeling experience.
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