Ajay Pal

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Questions related from Ajay Pal

NGSfastq seq analysis of Human Single Fold scfv Libraries I + J (Tomlinson I + J) ?

I am performing the NGS seq analysis of Tomlinson I + J phage library. The offical manual states that "Diversified (DVT) side chains based mainly on those positions which are diverse in the...

31 August 2023 4,553 0 View

Extract properties of mol2 molecules, along with properties using openbael or any other opensource ?

Hi I have mol2 datafile from molecular docking I am extracting molecules using openbabel obabel test.mol2 -O t.mol2 --filter "title='AK-968'" ########## last few lines of molecule mol2...

01 May 2019 3,106 3 View

Can a ligand induce de-/-phosphorylation ?

Hi Is it possible to design a small molecule (ligand - nonpeptidal) as a bridge/link between kinase and a mutated protein to phosphorylate the mutated protein. Say the kinase can phosphorylate...

07 March 2019 1,391 1 View

In silico pH predictor ?

Hi Are there any reliable pH predictors from 3d structure files of small molecules / liagnds ? Thanks

30 January 2018 5,047 0 View

Ligand_protein complex in Lipid Bilayer Gromacs MD simulation - diverging due to protin and liagnd constaints.

Hello I am running protein-ligand complex simulations- with protein embedded in lipid bilayer and solvated + ionized as per standard rules of Gromacs. After complete Energy minimization - in NVT...

01 January 1970 8,036 3 View