How Shall I perform Principle Component Analysis in GROMACS?

I have to perform PCA as a part of my results and analysis of protein-ligand complex docking using GROMACS 2018.8. How shall I perform PCA and interpret the results for the same? Any insights...

13 December 2020 3,121 2 View

How shall I prepare a protein PDB file in a particular pH for docking and simulation?

I wanted to prepare a protein at an alkaline pH for molecular docking as that is the pH I want to perform my in vitro assays in? I prepared my protein at the required pH through H++ server;...

13 December 2020 2,272 3 View

How to handle milk clotting Issues during media preparation for Screening of Halotolerant Protease Producing Bacteria (with Skim Milk)?

We want to screen halotolerant protease producing bacteria. Since Skim milk (HiMedia) is available in our lab, therefore, we want to screen extracellular protease by this compound/ supplement. We...

04 December 2020 7,657 6 View

What are the mechanism of actions of Ag and Cu nanoparticles on the bacteria and fungi?

We are assessing the activity of nanoparticle incorporated fabrics against bacteria and fungi.

24 November 2020 8,686 6 View

Has chemistry Nobel Prize really become the biology prize ??

07 October 2020 8,119 6 View

How to estimate nitrogen content (%) in plant using pelican equipment's KELPLUS ELITE-EX VA semi automatic kjeldahl distillation unit? ?

I am using KELPLUS ELITE-EX VA semi-automatic Kjeldahl distillation unit for nitrogen estimation. The salesman told me that unlike the older version; this version does not require making up the...

01 October 2020 844 3 View

Why Magnesium Sulfate is used in Loop-Mediated Isothermal Amplification(LAMP) reaction instead of MgCl2?

We have designed an in house LAMP assay for the detection of a pathogen. We have used ThermoPol buffer, betaine, MgSO4, Bst polymerase and dNTPs in the reaction. I wanted to know why MgSO4 is used...

22 September 2020 6,916 5 View

Which of the five PDB files (DRGFIN.PDB, DRGMMX.PDB, DRGNOH.PDB, DRGPOH.PDB & DRGAPH.PDB) as an output from PRODRG Server do I need to use?

I have some protein-ligand complex to simulate on GROMACS version:unchecked. For preparation of my ligands, I submitted the extracted Ligand.pdb file and submitted it in the Prodrg server, Energy...

01 September 2020 9,154 5 View

Can anyone please enlighten me, that what are free in silico toxicity prediction software/s available for academic purpose ?

Free toxicity prediction software based on genetic algorithm and deep learning of some training dataset #toxicity #Freesoftware #insilico #Deeplearning

30 August 2020 7,950 4 View

Cloning in TRV2 vector: tips?

So, I have been cloning a lot of genes over the years in various plant transformation and overexpression vectors and even though its a struggle always to generate positive clones, I usually am...

26 August 2020 8,364 9 View

Physics: Why do we describe light by referring to its wavelength, but microwaves and radar pulses by referring to their frequency?

In physics, the description of the properties of light generally refers to its wavelength (nm), while in the range of microwaves and radio waves we refer to the frequency of a signal (e.g. kHz or...

03 March 2021 1,682 3 View

Waters 2707 HPLC autosampler problem?

I am using a 2707 waters HPLC device. When I try to inject a sample, it says missing plate or rack. I changed the needle and calibrated its position but I still get the same problem. I even get...

02 March 2021 1,408 1 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Why Austenite grains in steel show much more twinning than ferrite grains?

It is oftentimes said to be a distinctive metallographic trait that differentiates a fully austenitic and a fully felly ferritic steel without etching that might distinguish between two. Why...

02 March 2021 728 2 View

Any research papers for extraction of nutrient deprivation on macroalgae? Analysed by HPLC-UV and GC/MS. Possibly from macroalgae genus Rhizoclonium?

I am doing my thesis on the nutrient deprivation on the macroalgae Rhizoclonium sp. I will be analysing the levels over a period of roughly 5 days by HPLC-UV and GC/MS. I will be using seawater as...

28 February 2021 6,477 1 View

What is the density for pva electrospining?

I'm Juan Carlos, a high school student who is working with electropinning, I made an electropinning machine with a 21g needle and a 30kv high voltage source and the distance between my needle is...

28 February 2021 298 3 View

Should we reduce the standard unit of length to 0.31951540592 meter ?

The reasoning behind this question is to align the ratios of the proton potential in energy per charge to the speed of light in distance per time. As these two dimensions appear to be related,...

27 February 2021 947 7 View

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View

How do you mesh a thin solid in Fluent?

Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the...

24 February 2021 8,856 3 View