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CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana

Gaihua Zhang, Yijing Zhang and Zhen Su*

Author Affiliations

State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100094, People’s Republic of China

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BMC Bioinformatics 2012, 13:332  doi:10.1186/1471-2105-13-332

Published: 20 December 2012

Additional files

Additional file 1:

Methods. Data collection and analysis, including the construction of a sequence profile for the BMCD pipeline, refinement of the initial A. thaliana CYPs model, docking, minimization and molecular dynamic (MD) simulation.

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Additional file 2: Table S1:

Metabolic pathways, substrates and products of the A. thaliana CYPs.

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Additional file 3: Figure S1:

The complexes formed between ABA and five different CYP707As. Figures whose AGI names end with “D” represent the last conformation following MD simulation for 50 ps. The key residues close to ABA are shown in a ball and stick model. The hydrogen bonds between ABA and residues of the protein are marked with green dotted lines and annotated with bright green words. For CYP707As, the majority of the hydrogen bonds are located between the ABA carboxyl and Lys78. After MD simulation of the ABA-CYP707A4 complex, a hydrogen bond formed between ABA C1’-OH and Tyr74.

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Additional file 4: Figure S2:

A schema for the CYPSI database. Eight MySQL tables found in CYPSI. The arrows represent the relationships between them.

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Additional file 5: Table S2:

The enzyme-ligand complexes and their key residues.

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Additional file 6: Figure S3:

The web interface for sequence similarity searching by BLAST.

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Additional file 7: Figure S4:

The BMCD server.

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Additional file 8: Table S3:

Methods comparison for CYP74A modelling.

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