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Questions related to Bioinformatics and Computational Biology
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 1,573 2 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 1,337 3 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 6,978 9 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 5,883 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 6,565 3 View
I did extraction of plant and i got crude extraction for petroleum ether, Chloroform, and methanol and I want to check the antibacterial activity for these three extractions. should I prepare...
28 January 2023 7,213 9 View
"TIME SENSITIVE-URGENT" I am running an MD simulation for an atomistic model with NAMD. I want to know the uses of plotting an RMSD curve for the equilibrated model. Is it only used for...
30 December 2022 3,525 3 View
I am looking up ways to decontaminate glass bottles from RNase and I came across several different methods, but have a lot of doubts about practicality. One comment under this post...
07 November 2022 6,475 3 View
Dear All, I have executed >1000 drug molecules in a Vina docking study. Now I have >1000 log files that contain the top ten binding scores for every compound in a log file for each. I want to...
07 November 2022 546 3 View
I have docked two proteins through GRAMM-X Protein-Protein Docking Web Server. Now, I want to perform MD simulation of the docked protein-protein complexes. I will be highly appreciated it if...
27 October 2022 5,604 3 View
I am interested to find interactions between plant wax and other chemical compounds. Is there any computational tool or webserver to find the interactions? Thank you
21 October 2022 9,615 4 View
I have... Independent variables :- 1. Seasons (Season 1 and season 2) 2. Treatments (6 groups) Dependent variable:- Number of grains Which statistical test in SPSS should I use? When I tried to...
17 October 2022 6,680 3 View
As usual Good quality Peer reviewed Reasonable APC (need not sell my kidneys for a paper) or Free Rapid review Good acceptance (not reject with universal stupid Submission declined...
15 October 2022 7,253 6 View
I have isolated svf from adipose tissues and will be characterising the macrophage using facs. I need to grow the isolated macrophages and need optimised protocol.
04 August 2022 6,201 1 View
For my research on the detection of Cr (VI), I must dilute my solution 3 times using 2 fold serial dilution to be able to analyze it with a UV spectrophotometer. So, I can calculate the 3 times...
22 April 2022 3,768 5 View
I have completed my molecular dynamics (MD) on three complexes and protein alone. All the three complexes have Higher RMSD value than the protein alone. How can we justify this Higher RMSD of...
10 April 2022 7,321 2 View
Autodock Vina- Error in docking
21 December 2021 6,711 1 View
When I load repeat simulation of my mutated protein from 10ns-20ns-30ns, its RMSD graph is in picture. I watched my dcd, my protein goes out of the water box. I tried to put it inside of the box...
15 May 2020 589 6 View
Few of us wanted to create a discord server for Biophysics. What we intend is to begin a commonplace for discussions/numerical experiments. Also possibly document the results in the form of blogs...
02 April 2020 7,177 3 View
I am working on FIV and have sequenced each gene individually and retrieved multiple complete genomes and individual genes from Genbank. I am trying to align all the different genes to the...
03 March 2020 1,536 1 View
Hi everyone! I've been study the expression of 5 microRNAs using TaqMan assays in several cell lines (microRNAs were selected through literature review) and I obtained statistically significant...
02 February 2020 7,574 3 View
Hi, Can anyone please explain me how to use Genscan tool to find exons and introns for a given gene sequence? I want to calculate sensitivity and specificity to check its performance for a given...
31 December 2019 2,193 3 View
Hi! I've been using the refine.bio website to download normalized transcriptome data; each downloaded dataset consists in a compressed directory with an expression matrix in .tsv format, its...
12 December 2019 6,351 2 View
12 December 2019 4,919 3 View