Can anybody tell me about the basic principle behind the use of neutral and alkaline comet assay ?

In most of the research paper people used both neutral and alkaline comet assay to determine the level of DNA damage either single stranded or double stranded but the exact principle of both the...

02 August 2020 2,193 2 View

Any suggestions on what kind of statistical analysis should I do with a sample size of 100?

I have done a short survey and until now, I was able to collect only 100 responses. Not sure if collecting more would be possible. So was wondering, what kind of statistical analysis would support...

20 July 2020 9,629 12 View

After regression, how to command STATA to star above significant coefficients at 10%, 5%, and 1% levels (two-tailed) and (one-tailed)?

i am using STATA for thesting my hypotheses, what is the right command should i write to get star above significant coefficients at 10%, 5%, and 1% levels (two-tailed) and (one-tailed)? i...

09 April 2018 2,251 10 View

How would I do MM-PBSA analysis after MD simulations in GROMACS?

27 January 2016 5,610 9 View

How do I perform Pharmacokinetic study through computational softwares? Is there any online server or any freely available software for it?

I need to perform QSAR and pharmacokinetic study in silico. Please guide me with any server or software which i can freely access and which is quite reliable as per results are concerned.

17 December 2015 301 12 View

Which metals ions form complex with sodium potassium tartrate?

Can +3 cations form tartrate complexes?

25 October 2015 3,094 3 View

How might I calculate Guanidinium concentration in molecular dynamics simulation of proteins?

Hi everyone!! While performing the MD simulations on proteins and studying their unfolding by Guanidium, How should one determine the guanidium concentration with regard to the number of molecules...

29 July 2015 4,437 5 View

Is it possible to study the interaction of a ligand with DNA at different pH conditions through a molecular docking approach?

A ligand showing different effect at different pH. I wanted to study the interaction of the ligand with DNA. So how will i study those at different pH environment through molecular docking...

09 October 2014 5,874 3 View

Can someone help me to estimate change in phosphate concentration in mouse macrophage cell line before and after bacterial infection?

I have used malachite green phosphate estimation kit but its sensitivity was not appropriate as per requirement.

26 May 2013 9,752 2 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How can I make a center of mass vs time graph?

I have a trajectory file of about 1000 frames which I have calculated a center of mass for each frame. I would like to use the first frame as a reference and see how much the center of mass...

04 February 2021 5,774 1 View

How do you get around this AutoDock Vina error?

I get the following error messages after running the simulation: Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7 AutoDock Vina ligand docking initiated for...

26 January 2021 3,822 3 View

What is the best way for mobility estimation in GROMACS?

I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...

19 January 2021 531 3 View

How to generate .dlg files on PyRx?

Hi. I'm using the PyRx version 0.8 and getting the error message: WARNING: Filename mismatch: "2DFN_ADP_CL.maps.fld" :: "..\2DFN_ADP_CL.maps.fld" C:\Program Files (x86)\The Scripps Research...

17 January 2021 843 3 View

Does GROMACS gmx trjconv sometimes leave a split in a protein?

I have been processing some trajectory files from my molecular dynamics simulation using GROMACS by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein...

30 December 2020 849 4 View

Is there any online webserver for DNA-ligand docking?

I have used Autodock 4.2 for docking studies and trying haddock for DNA-Ligand docking. It shows an error and not supported DNA PDB file. Suggest a template for DNA and ligand PDB file and also...

29 December 2020 1,322 8 View

Autodock Raccoon - the following maps are missing?

I've generated a set of maps for my receptor using ADT (AutoDockTools). It has resulted in the files: .A.map .C.map .HD.map .N.map .NA.map .OA.map .SA.map .d.map .e.map But when I try loading the...

20 December 2020 7,721 2 View

How to specify binding sites in AutoDock Raccoon?

Hi all, There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result. This is concerning Raccoon(1) original, not Raccoon2. The original...

17 December 2020 4,302 2 View