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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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Updated: Nov 5, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking.

Hui Wang1,2, Qian Wang2,3, Yuqian Liu2,4

  • 1College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.

Synthetic and Systems Biotechnology
|May 17, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces a new computational process to predict plant cytochrome P450 structures and screen their functions. This aids in discovering and engineering valuable plant P450 enzymes for natural product modification.

Keywords:
DatabaseHomologous modelingLigand dockingPlant P450 databaseWeb service

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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.