PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Plant cytochrome P450s are crucial for modifying plant natural products.
• Limited crystal structures hinder the study and engineering of these vital enzymes.

Purpose of the Study:

• To develop computational methods for predicting plant P450 structures and functions.
• To create a database and web service for plant P450 analysis.

Main Methods:

• Combined Rosetta homologous modeling and MD-based refinement for structure prediction (PCPCM).
• Developed a ligand docking process (PCPLD) for virtual screening.
• Constructed a plant P450 database (PCPD) with sequences, structures, and functions.

Main Results:

• Successfully applied PCPCM to 181 plant P450s.
• PCPLD reduced virtual screening space by approximately 80% in test cases.
• Established PCPD (http://p450.biodesign.ac.cn/) and a web service.

Conclusions:

• Developed novel methods for P450 structure analysis and functional prediction.
• Introduced a universal approach to assist in mining and analyzing plant P450 enzymes.