Protocol for predicting γ-tocotrienol and δ-tocotrienol binding to colorectal cancer-related proteins using Schrödinger’s Maestro and Glide
Year: 2025
Type: article
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. • Protein structure refinement steps before docking analysis • Ligand protonation, stereoisomer generation, and conformer expansion • Defining binding pockets through receptor grid generation protocols • Execution and evaluation of protein-ligand docking and binding poses Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.
Source: STAR Protocols
Institutions: Monash University Malaysia, IMU University
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $1,550
Award: G1574763320
OpenAlex ID: W4415317106