1. Beware of docking! Trends in Pharmacological Sciences
Yu-Chian Chen 
Trends in Pharmacological Sciences 
Volume 36, Issue 2, Pages (February 2015)
DOI: /j.tips
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2. Figure 1
The increase in the number of papers, from 1990 to 2013, retrieved from the PubMed Central (PMC)-NCBI database ( Keywords were ‘docking’ or ‘dock’ shown in the abstract or title.
Trends in Pharmacological Sciences  , 78-95DOI: ( /j.tips )
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3. Figure 2
All docking publications from 1990 to Autodock, GOLD, and Glide are the most-used docking programs.
Trends in Pharmacological Sciences  , 78-95DOI: ( /j.tips )
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4. Figure 3 Flow chart of the docking procedure.
Trends in Pharmacological Sciences  , 78-95DOI: ( /j.tips )
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5. Figure 4
The docking mode can be roughly divided into four types of docking mode.
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6. Figure 5
The ligand, angeliferula, is docked well into the binding site of protein phosphatase 2A (PP2A), and with the highest dock score. There is a clear difference between the docking pose and the final ligand pose after a molecular dynamics (MD) simulation of 20ns [183].
Trends in Pharmacological Sciences  , 78-95DOI: ( /j.tips )
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7. Figure 6
The ligand, dichotomoside E, is docked well into the binding site of protein phosphatase 2A (PP2A), and has the highest dock score. There is also a clear difference between the docking pose and the final ligand pose after a molecular dynamics (MD) simulation of 20ns [183].
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8. Figure 7
The ligand, FOG1, is docked well into the binding site of retinoblastoma-associated protein (RbAp48), and with the highest dock score. Again, there is a clear difference between the docking pose and the final ligand pose after a molecular dynamics (MD) simulation of 20ns [184].
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9. Figure 8
The ligand, ningposides C, is docked well into the binding site of histone deacetylase 2 (HDAC2), and with the highest dock score. As before, there is a major difference between docking pose and the final ligand pose after a molecular dynamics (MD) simulation of 20ns [181].
Trends in Pharmacological Sciences  , 78-95DOI: ( /j.tips )
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10. Figure 9
Flowchart of computer-aided drug design (CADD). The protocol is divided into three parts: structure-based drug design, ligand-based drug design, and validation by molecular dynamics simulation.
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11. Figure 10
The possible four modes for drug design in silico. Case (A) shows a ligand with rapid docking in the binding site and also a long residence time in molecular dynamics (MD) simulation. Thus, it might exhibit superiority as a potent lead. In case (B) the ligand has a lower dock score but a long residence time. In (C) it shows rapid binding with a high dock score but with a short residence time. The total occupation time is short; however, this might not be disadvantageous because the ligand can bind again quickly. Theoretically, case (D) is not a good candidate because it shows a lower docking speed and short residence time.
Trends in Pharmacological Sciences  , 78-95DOI: ( /j.tips )
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