AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

Key Points

• To introduce and evaluate AMBER, a flexible computational program designed to construct molecular models and calculate inter- and intramolecular interactions using empirical energy methods.
• Implemented empirical energy calculation algorithms capable of modeling small chemical compounds as well as large polymers.
• Simulated rotational isomerism across D-Val, L-Pro, and L-Pro-Sar amide bonds in actinomycin D.
• Evaluated energy profiles and structural conformations comparing the theoretical Sobell model with actinomycin D X-ray crystallographic structures.
• Demonstrated a generalizable molecular modeling framework capable of energy refinement across diverse molecular scales.
• Characterized conformational energy barriers and rotational isomers for specific amide bonds within actinomycin D.
• Resolved structural and energetic differences between proposed theoretical models and empirical X-ray diffraction data.