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Questions related to Bioinformatics and Computational Biology
I performed a dynamic simulation of an aptamer-protein complex using the Namd software, and I want to the calculate the RMSD value using vmd
16 February 2024 5,957 1 View
I'm doing several steps, such as minimization and equilibration, to start running MD simulations and I'm trying to automate this process by running one step after finishing the other. When I go...
11 February 2024 7,667 1 View
I'm trying to perform MD simulation of protein-ligand complex. The step5_production.inp was set for 100ns. After running for around 30ns the program stop automatically. How will i modify the file...
07 January 2024 1,468 1 View
Hello, I have performed a simulation of Sodium Montmorillonite swelling due to water adsorption. However, I am not sure if the simulation is correct. I followed the following steps: 1. A model of...
18 December 2023 9,962 1 View
Hello, I hope you are well, I have been searching and I cannot find the components to make an RNase decontamination reagent in the laboratory, without having to buy the RNase away. Thanks
27 September 2023 5,320 1 View
-20 C dilution
02 August 2023 152 0 View
hello I have done a 50ns MD simulation production run on three different protein-peptide complexes. unfortunately, I am getting quite a high RMSD in all of them. I tried many things but couldn't...
25 July 2023 1,593 2 View
I tried a number of Trizol and kit based protocols. None is high yield and reproducible. Anyone who has done it before and have a very good working procedure?
24 July 2023 3,908 0 View
We are isolating cells from nasal lavage fluid and saving them for RNA extraction. We recover between 20,000 and 1 million cells and would like to use a lower volume if it will not affect our RNA...
20 July 2023 7,356 0 View
Could you explain the process by which the RMSD result is created, and provide insight into any noticeable jumps or fluctuations in the data? I'm curious about the underlying reasons behind these...
10 July 2023 1,358 3 View
Hello! I want to give a brief overview of my research (it's a thesis) for a better understanding of my "problem". I have three research questions: RQ1: it holds two hypotheses both using the...
08 July 2023 7,945 2 View
For my thesis I'm doing data analysis about the relation between Sensory Processing Sensitivity (measured by total score on SPSQ) and internal (measured by 8 dimensions of MAIA) and external...
02 July 2023 162 2 View
Is basic knowledge essential for it!
02 July 2023 236 3 View
I encountered an article that is about enhanced sampling method of protein - ligand system. The paper is 'Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand...
02 July 2023 1,256 1 View
I am trying to find some effective epitopes on the protein IL13R alpha 2 . What a method that I should follow ?
12 June 2023 7,302 1 View
Our team is participating in igem competition. We're going to use a plasmid with a part of the gene on it that expresses a protein we don't need(GST-tag). We worry that such a protein will affect...
09 June 2023 7,377 3 View
In my lab our primer stock came from two different manufacturers, in particular the housekeeping primer is not from the same brand as the target primer. Do you think this would be an issue? I'm...
25 May 2023 9,121 2 View
I am working on a molecular dynamics simulation in protein-ligand system, using NAMD software, and I got the following error. "FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HGA1 CG3C51 SG311...
21 April 2023 1,425 5 View
The temperature of keeping eggs is 27 degrees Celsius and the humidity of the environment is 70%.
20 April 2023 9,138 1 View
Hi all, Please suggest how I need to optimize a small molecule to generate the topology file for the ligand to process it for Protein-Ligand MD simulations. I have tried to balance the valency of...
12 March 2023 7,000 9 View
I have thousands of samples from `TCGA` retrieved using `TCGABiolinks`. I want to remove the `batch effect` from the datasets. It's mentioned that batch can be detected from sample ID itself How...
09 March 2023 3,426 0 View
i am trying to show the van der waals interactions between a drug and its active site in pymol. i am able to display polar interactions such as hydrogen bonds, how ever i do not know how to...
04 March 2023 5,914 1 View
I have a .pdb file with me and when I try to open that file in PyMol, I see some unusual dashed lines at the end of the chain. It seems like the last amino acid is stretched. how can it be...
14 February 2023 6,583 3 View
Hello, I am currently starting to use mesenchymal cells derived from adipose tissue, I want to study their immunoregulatory properties. How to choose the best panel of anti and pro inflammatory...
31 January 2023 7,427 0 View