Web-ARM

Web-ARM automates construction and analysis of QM/MM models of rhodopsins to enable prediction and study of their photophysical properties.

Key Features:

• Automated Model Construction: Utilizes the python-based a-ARM protocol to generate QM/MM models from crystallographic structures or comparative models provided in PDB format.
• Excitation Energy Calculations: Computes excitation energies at the CASPT2//CASSCF/Amber level of theory to predict trends in UV-vis absorption maximum wavelengths.
• Mutant and Variant Screening Support: Provides rapid model generation to support screening of rhodopsin mutants and variants for photophysical property prediction.

Scientific Applications:

• Structural and Functional Analysis: Enables exploration of the structural and functional dynamics of rhodopsins, including the effects of mutations on protein behavior.
• Photophysical Prediction and Color Tuning: Supports prediction of UV-vis absorption maxima and investigation of rhodopsin color tuning mechanisms.
• Mutant Screening and Variant Design: Facilitates screening and comparison of rhodopsin mutants and variants to identify candidates with desired photophysical properties.
• Education and Training: Provides practical, model-based exercises for teaching concepts related to photochemistry and rhodopsin function.

Methodology:

Automated generation of QM/MM models via the python-based a-ARM protocol from crystallographic structures or comparative models in PDB format, and computation of excitation energies at the CASPT2//CASSCF/Amber level to predict UV-vis absorption maxima.