18 Questions 49 Answers 0 Followers
Questions related from Sourav Pal
When checked in enzymatic assay, a compound with IC50 37 nM showed a KD value of 20 µM against ITC. I would like to know how can this discrepancy be explained? Thank you in advance.
18 July 2023 8,314 5 View
I am trying to find out the logic in not identification of hydrogen bond interaction in the charged NH+ from the ligand part with the Asp residue from the protein. That incidence has been observed...
01 June 2023 7,388 0 View
I have synthesized a racemic compound and its two enantiomers. The IC50 value of racemic compound is 2.4 μM, for R is 1.1 μM and for S is 0.5 μM against the target protein. How to explain the...
11 May 2023 9,469 7 View
I have been using the 2D QSAR modelling by QSARINS software. I cannot find the final equation of the developed QSAR model. Kindly guide me. Thanking you in anticipation.
27 December 2021 8,809 0 View
Hello, I already made a ligand-based pharmacophore by utilizing 60 dataset compounds by catalyst module in discovery studio. But I want to explore the ROC curve of that pharmacophore in order to...
03 March 2020 9,322 5 View
I want to perform molecular dynamics of protein-ligand complex simulations by amber force field. but my ligand conatins 3 protonated amine. so can help me how to make the topology and parameter...
25 September 2019 5,260 10 View
I want to perform a protein-DNA-ligand complex simulation by gromacs. but my system contain two ligands named PTR and LIG. but when ever i am going to perform the energy minimization. This is...
24 December 2018 7,151 4 View
I want to do GROMACS simulation using ffamber_99sb forcefield. so that i have to generate the topology of the small molecules by ACPYPE. So can you tell me how to install ACPYPE and Anteamber...
17 December 2018 8,286 7 View
I have a trimeric protein which have a lots of missing residues. that why i decided to build homology modelling. but after successfully modelling each chain contains maximum loop like structure...
09 April 2018 3,466 4 View
Actually I want to build a homology model of a human homotrimeric protein from a FASTA sequences. After BLAST I got a template which is 91% identical but it is originated from Mouse organism. and...
16 January 2018 3,122 6 View
I have a protein containg 2138 amino acids in each chains. then i added POPC membrane and then add solvent ater and counter kcl ions..then i had done 025ns run for eqilibration by restrating...
18 September 2017 6,986 4 View
Hello Everyone, I have a AUTODOCK docking PDB file for both Protein-Ligand-DNA Complex. I want to do simulation of these complex. but simulation failed due to unrecognized ATOM TYPES present into...
15 June 2017 9,149 4 View
actually i am new in gromacs, i started to follow the protein ligand simulation tutorial from gromacs server, but there i cant understand how will i make the topologies from PRODRG webserver. can...
01 June 2017 3,629 15 View
Dear All After running the NAMD for around 2ns the following error is coming. Could any of you please help me in this regard. "FATAL ERROR: Unable to open text file ions.restart.xsc: File...
29 April 2017 9,443 7 View
i want to perform steered molecular dynamics by using TCL script. but it failed during showing this message: FATAL ERROR:Cant used non-numeric floating point value as operand of "-" while...
26 January 2017 2,876 2 View
we didn't find any specific TLR7 specific antagonist . maximum are dual antagonist of TLR7 and TLR9 antagonist. Is there any specificity on the protein active site? what was the reason for that?
05 September 2016 4,593 6 View
I have to prepare a PBC box. the cell basis vector is 178 0 0 , 0 178 0, 0 0 185. please can anyone suggest me what will be the PBC grid size?
17 August 2016 6,320 0 View
i want to perform steered molecular dynamics on a channel protein for opening up their gating pathway. for that reason i want to apply a force on multiple atom (E.g minimum 2 amino acid...
12 August 2016 10,084 3 View
