20 Questions 41 Answers 0 Followers
Questions related from Rajiv Lakkaniga
Hello, I am a beginner in molecular dynamics, and am considering to use Metadynamics to address one of the questions about protein structure in my research. I would appreciate if the RG community...
10 October 2023 5,650 1 View
Say there is a -NH....F hydrogen bond possibility in a protein ligand complex. How strong will this bond be in comparison with -NH....O or -NH....N ?? Also, if this fluorine is attached to a...
18 June 2020 4,813 11 View
Most of the publications which show a molecular docking model focus mainly on hydrogen bond interactions, pi-pi stacking, cation-pi stacking interactions. How significant are the hydrophobic...
08 May 2020 9,276 3 View
I am trying to synthesize a compound which has both carboxylic acid and amine. During the purification, when I do the pH adjustment it forms a zwitterion and goes into the aqueous layer. Is there...
20 February 2020 4,045 6 View
I am looking to publish part of my medicinal chemistry project as a communication article. I am looking for journal impact around 5-6. Any suggestions? Thanks.
30 January 2020 7,996 4 View
I am working on computationally understanding the active and inactive conformations of some proteins. Simulating the inactive conformation from the active conformation is reported in literature by...
23 October 2019 5,944 2 View
Are there any bioisosteric replacements of triple bond (alkyne) which were employed for lead optimization or scaffold hopping? Thanks.
24 April 2019 2,814 4 View
I have previously done sonagashira coupling of aryl bromides, with Pd catalyst and CuI in triethylamine solvent at 70C. The reaction was clean with very good yield. I tried the same conditions for...
14 April 2019 5,864 3 View
I am trying to synthesize boronic acid pinacol ester derivatives from aryl/hetero-aryl halides. Is there any TLC staining technique which can indicate the formation of boronic acid? Thanks.
04 April 2019 4,314 11 View
I have a protein ligand complex. How can I calculate the contribution of the individual residues to the overall binding of the inhibitor in the protein's binding pocket? I need it in two cases:...
29 October 2018 4,366 5 View
I have imported a MD trajectory in VMD. I need to generate plots like how the distance between two selected atoms is changing over the simulation. Is there a way to do this in VMD? Thanks.
22 August 2018 2,804 3 View
I am trying to do metadynamics simulation for my protein. Can someone explain what is a collective variable, and on what basis we decide collective variables in a metadynamics run? Thanks.
01 August 2018 4,152 3 View
Is there a way to computationally predict the membrane permeability of small molecule protein inhibitors? I am not looking for 'absolute' values. I need to figure out relative permeability of two...
09 June 2018 3,066 4 View
I am trying a coarse-grained simulation in gromacs to understand certain protein folding. I initially tried with triclinic box and -d 1.0. I used -c to center my protein in the solvent box. But...
31 May 2018 6,010 4 View
Hi, I want to do an all-atom MD simulation without adding bias to a protein kinase. My starting conformation is DFG-in. How many nanoseconds of simulation is required, for the activation loop to...
25 March 2018 7,536 3 View
Hi, I am trying to run a MD simulation of a protein-ligand complex in a cluster. The npt run is complete and the log file doesn't show any error. Next the grompp also runs, without throwing any...
09 March 2018 7,832 5 View
I know some computational chemists who generate many, like a hundred, different conformations of the ligand to dock it the protein. I use Glide, and it considers ligand flexibility. So, it is...
21 February 2018 4,430 4 View
I have an active molecule and want to determine its binding pose in the target protein. I have docked the molecule using two different crystal structures of the same protein. But I got two...
20 December 2017 8,078 13 View
I have been using autodock vina and Schrodinger for molecular docking. Many times, molecules with a higher IC50 show better interactions and a lower score than the molecules with lower IC50. So,...
09 February 2017 8,678 8 View
Autodock takes the input form only in .pdbqt. This format is accepted in no other software. How to prepare the ligand in AutoDock Tools? When i prepare the ligands in other software and import it...
01 January 1970 9,882 5 View
