How to calculate the DNA-protein interaction energy from GROMACS MD trajectory ?

17 August 2023 0 3K Report

How to determine the interaction energy between DNA and protein in a DNA-protein complex for any type of bonded (H-bond) and non-bonded (electrostatic, salt bridge, etc.) interactions?

Badges
Science topic

More Kanika Kole's questions See All

Can anyone share any official document (any UGC Notification or so) for supporting PhD transfer from one University to other?

11 July 2023 4,083 2 View

How do you make RIPA buffer without detergent in the lab?

I am trying to make mouse adipose tissue lysates and I want to first make homogenates using RIPA buffer without any detergent to avoid foam. As I am adding sodium deoxycholate, it’s precipitating...

20 May 2023 7,473 0 View

Where can I find normal reference values/range for serum cholesterol levels (total, HDL and LDL) in mice?

I have cholesterol levels (total, HDL and LDL) for male and female hypertensive mice and want to compare them with normal reference values for cholesterol for male and female mice to compare my...

12 March 2023 9,081 1 View

Can any one provide me catalog number of LPS and interferen gamma for the stimulation of RAW 264.7 in terms of nitric oxide production?

can any one provide me catalog number of LPS and interferen gamma for the stimulation of RAW 264.7 in terms of nitric oxide production?

02 March 2023 7,965 0 View

What is the difference between Taqman Universal master mix and Taqman gene expression mastermix ?

I have FACS sorted some different types of immune cells (Innate lymphoid cells, gamma delta T cells, Natural killer T cells and Natural killer cells). As the number of cells were less in number, I...

21 January 2023 3,778 0 View

Can we use Principal Component Analysis for Likert scale variables?

Respected all I have been trying to formulate Financial Inclusion Index based on primary data where many variables like quality of credit, bank credibility etc. are measured in Likert scale of...

06 June 2022 3,710 6 View

What should be the procedure to refold an alpha-helical membrane protein?

The protein was in inclusion bodies and I solubilized it in 8M urea. I employed dialysis to remove urea and to refold the protein. Unfortunately, it formed aggregates.

12 September 2021 428 4 View

Do we suggest Post exposure prophylaxis for rabies to a calf??

If a calf say of 7 days old got bitten by a rabid suspected dog then what should be the course of action except euthanasia?

25 August 2021 1,907 4 View

I am looking for a good course of python relevant for biologists that should encompass machine learning and big data analysis. Any suggestions?

I am aware of the book by Martin Jones. Any other suggestions preferably of an online course with good reviews and certification would be great.

11 May 2021 648 5 View

Role of pH in RBC lysis solution?

Role of pH in RBC lysis solution I want to ask aquestion in context of RBC lysis solution used in flow cytometry We have been using our own lab made lysis solution containing ammonium chloride...

07 March 2021 5,070 3 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Basis set and input instruction to calculate HOMO and LUMO using Orca for Imidazolium based organic salts?

Hey there, As a synthetic chemist delving into theoretical calculations for my imidazolium-based organic molecules, I would greatly appreciate any guidance on the appropriate input instructions...

09 August 2024 5,444 7 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

How can I apply boundary conditions in an orthotropic steel deck numerical model using ABAQUS software?

I am trying to simulate vehicular loading on an orthotopic steel deck bridge section in ABAQUS software. The red arrow mark in the attached figure indicates the direction in which the vehicle will...

08 August 2024 719 0 View

Does crude extraction using NaOH and Tris work well with Fungi?

I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you

08 August 2024 4,733 2 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 3 View

Can anyone explain why there is not any color bands in the middle portion of the tensile coupon?

Details of the Analysis. Static Analysis Composite Layup Continuum Shell Elements FRP Material (Elastic and Hashin Damage)

03 August 2024 8,538 4 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View