Uddipta Ghosh Dastidar

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Questions related from Uddipta Ghosh Dastidar

Why the Biological Activity (IC50) of my Racemic molecule is greater than both of its individual pure enantiomeric components?

I have an active small molecule inhibitor of an enzyme. The S enantiomer has IC50 0.5 µM. The R enantiomer has IC50 1.1 µM. But the racemic has IC50 2.4 µM (i.e. less active than both R and...

11 May 2023 1,559 6 View

EPIK Ionization Penalty in Schrodinger Maestro: Less or More; Which is favourable?

In the LigPrep module of Schrodinger Maestro, using EPIK, several ionization states are generated for a single molecule. To choose among them according to ionization penalty values, are the states...

21 February 2023 9,799 0 View

Why in GROMACS MD, proteins chains are separating suddenly instead of gradual shifting?

I am using GROMACS 5.1.5, for MD simulation of a dimeric protein to study the gradual separation of two chains. However, in certain frames (as seen in VMD) the chains are suddenly completely...

01 December 2022 4,362 9 View

How to index two same ligands separately, attached with two chains of dimeric protein in Gromacs for MD simulation?

I have a homodimeric protein (Chain A & B) in complex with two same ligands (LIG1 & LIG2) for MD simulation in Gromacs. I have created separate ITP files for both ligands and the MD has completed....

01 December 2022 6,528 6 View