The article of Ahmed and co-workers is worthy in its scientific content, however, I have some confusions regarding the parameters used in docking study,
1. Authors have not described from which pacakage they had used the TOPCAT for toxicity prediction. Since TOPCAT is a part of Discovery Studio and authors have not mentioned this.
2. As authors have mentioned, they have used GLIDE for docking, then how they got the docking results in the scoring functions like LigScore1, LigScore2, PLP1, PLP2, Jain, PMF and Dock Score instead of Glidescore. These scoring functions are not as a part of GLIDE. They have not discussed about Glidescore.
3. The sentence used by the authors '.... molecular docking analysis was performed using ligand fit of GLIDE software from Schrodinger ..'. Make it clear, Is it correct to quote this.
3. As discussed in docking with Glide, it does not work with the structure itself but with a grid representing the properties of the structure (i.e. electrostatic potential generated on each grid points, van der Waals etc…), but authors have not discussed the grid preprations.
4. Further in the last line of Docking analysis section '....All the compounds/ligands which forms good hydrophobic and hydrogen bond interactions with Phe163, Asp199, Val200, Phe203, Met228, Glu255, Pro257, Phe281, Asp285, Asp329 and Arg415.' What does it means.
5. At last, the docking study is seems to be quite ambiguous.
Docking Study Regarding
25 July 2014
The article of Ahmed and co-workers is worthy in its scientific content, however, I have some confusions regarding the parameters used in docking study,
1. Authors have not described from which pacakage they had used the TOPCAT for toxicity prediction. Since TOPCAT is a part of Discovery Studio and authors have not mentioned this.
2. As authors have mentioned, they have used GLIDE for docking, then how they got the docking results in the scoring functions like LigScore1, LigScore2, PLP1, PLP2, Jain, PMF and Dock Score instead of Glidescore. These scoring functions are not as a part of GLIDE. They have not discussed about Glidescore.
3. The sentence used by the authors '.... molecular docking analysis was performed using ligand fit of GLIDE software from Schrodinger ..'. Make it clear, Is it correct to quote this.
3. As discussed in docking with Glide, it does not work with the structure itself but with a grid representing the properties of the structure (i.e. electrostatic potential generated on each grid points, van der Waals etc…), but authors have not discussed the grid preprations.
4. Further in the last line of Docking analysis section '....All the compounds/ligands which forms good hydrophobic and hydrogen bond interactions with Phe163, Asp199, Val200, Phe203, Met228, Glu255, Pro257, Phe281, Asp285, Asp329 and Arg415.' What does it means.
5. At last, the docking study is seems to be quite ambiguous.
Competing interests
None