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Figure 1 | BMC Bioinformatics

Figure 1

From: Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes

Figure 1

Study design and overall workflow. BLAST was used for the rat AFP protein sequence against PDB to select a template sequence for homology modeling. The initial 3D structure obtained from homology modeling was further optimized using MD simulation. The optimized 3D structure was used as the docking receptor. Thirteen structurally diverse rat-AFP binders were selected from our recently reported results [4] and were docked into the receptor. Finally, the ligand binding free energy for the complex was calculated based on the MD simulations.

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