23 Questions 85 Answers 0 Followers
Questions related from Alireza Mohebbi
Dear ResearchGate community, I have recently conducted two separate 100 ns molecular dynamics simulations using GROMACS, each involving a small molecule. My analysis of hydrogen bonding patterns...
18 November 2023 3,319 5 View
To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...
02 March 2021 9,316 4 View
If someone uses a cut-off ELISA kit, is it possible to use the ODs for comparison of sample data to control groups and not only report positive and negative?
27 October 2018 578 3 View
Hi there, I need to import a DNA molecule into a crystallographic pdb file containing a viral capsid. Furthermore, I want to add some ion molecule surrounding the viral structure. Is there any...
20 August 2018 4,712 4 View
Hi there, I have a stock solution of a clinical isolated phage with a titre of ~3E12 pfu/ml. Is it high enough for TEM microscopy, and is there any other considerations for imaging? Regards Alireza
24 June 2018 9,355 2 View
Hi, I have extended my MDS using Gromax according to this: gmx convert-tpr -s md_1.tpr -extend 9400 -o md_2.tpr gmx mdrun -s md_2.tpr -cpi md_1.cpt -nb gpu -v However after simulation done, I...
28 May 2018 5,305 4 View
Hi, I have used a magnetic-based DNA extraction kit. At the final step, when I want to dissolve DNA from magnets in elution buffer (Triss-EDTA pH=8.5), the magnet dyes are dispersed into the...
13 January 2018 7,528 4 View
Dear all, Hi, As it is shown in the attached figure, we have dsRNA on a PAGE. However, the wavy bands and skewing on the left-side of the columns have made some disturbances. How can we prevent...
12 November 2017 2,752 4 View
Hi, I want to ask you how can I be sure if my assembly is quite right?. I 've used NGS assembly using AbySS followed by QC-check. Regards
29 July 2017 4,799 5 View
Hello, I have sequenced an organism by using NGS technology. After assembly, I found it only has 6-22% homology with other related GenBank enteries. I performed MSA with all of related-organism...
29 July 2017 8,755 2 View
Hi, I want to know if there is any databases containing integrated genomic data of patients with psychiatric or mental illneses. If there is none, does it resonable to make one? Regards Alireza
18 April 2017 526 1 View
Hi there, I have recently assembled a NGS HiSeq data with ABySS 2.02. With the default setting (K-mers=64) I had a 183nt stretch of N (or Gap). I have changed k-mer to 40 and the gap reduced to...
15 April 2017 1,051 3 View
Hi, I have a un-crystalized viral capsomer and I want to predict its 3D strucure. I used Phyre-2 for predicting the structure. However, when I wanted to transform it into high-order structure, it...
25 February 2017 5,307 5 View
Hi, I want to perform the last step of Molecular Dynamic Simulation (MDS) with different.mdp parameters by gromacs 5.1.4. Do I have to change all post-steps parameters, including EM and...
28 January 2017 1,753 3 View
Dear researchers, We want to analyze autophagy in breast cancer cell line, MCF-7. I have searched for bec-1 expression but didn’t find any results. Therefore, if anyone has already investigated...
17 January 2017 7,457 3 View
Dear Researchers, Hi, I tried to analysis Van der Waals and electrostatic energies of a receptor complexed with a ligand. As illustrated in attached figure, gromacs energy module brought me 73...
10 December 2016 1,931 11 View
Hi there, I have a DNA sample size of 152 sequences with sparse in their length. I want to construct a Maximum likelihood-based phylogenetic tree using PhyML 3.0 but first time it gave me an error...
17 September 2016 818 2 View
I have a series of ligands specifically to a certain receptor. Annotated data correspond to the receptor experimentally define mutations which lead to 75-200 fold affinity reduction....
07 September 2016 3,310 5 View
I did a double digest on a TA cloned vector and putted the insert in an other expression vector, pcDNA3.1+. As it is shown in figure, three first wells are plasmid extracted colonies for which PCR...
12 July 2016 3,265 4 View
As it is difficult to extract RNA from old-aged Formalin-Fixed, Paraffin-Processed tissue, I wonder if it is possible to culture tissue, do you think it is possible? Thank you
14 May 2016 9,913 3 View
How much should be the concentration of SDS, EBr, and Acridine Orange for plasmid curing in anribiotic resistant Vibrio species?. Do these solution necessarily kill bacteria for plasmid curing, or...
27 September 2015 3,293 3 View
I have a prolem with my PCR products. For the fist time I used PCR then tooke the products on gel electrophoresis, with the published protocol, my results became positive. For the next time the...
15 August 2015 2,576 9 View
Dear Researchers, Hi, I have performed an MD simulation with Gromacs 5.1.4. Now, I want to make a movie of simulation. After loading .xtc and .gro files into VMD 1.9.3beta1, I was able to create...
01 January 1970 9,045 4 View
