25 Questions 55 Answers 0 Followers
Questions related from Alireza Mohebbi
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?
10 October 2018 7,681 4 View
Hi, Recently, I performed a MDS with Gromacs and did not neutralized the system. MD was ran and nothing happened. I wonder what will happen in a non-neutral MDS. Can it be used for analysis? Regards
09 September 2018 6,524 4 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...
08 August 2018 8,612 5 View
Hi, I have a single-stranded circular DNA with ~6k genome size. I want to choose a good DNA Seq platform. Can anyone help me with that please? Regards, Alireza
07 July 2018 8,256 2 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
06 June 2018 1,151 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...
05 May 2018 2,803 5 View
Hi there, I have a forest plot of a meta-analysis. From 13 studies with same method and same subjects I have 2 studies in same country, which are outliers. The studies have two different sample...
04 April 2018 599 9 View
Hi, I have extended a simulation from 10ns to 100ns with following command: gmx convert-tpr -s md_10ns.tpr -extend 90000 -o md_100ns.tpr and: gmx mdrun -s md_100ns.tpr -cpi md_10ns.cpt -nb gpu...
03 March 2018 553 1 View
Hi there, I want to know how can i determine fluctuations, flexibility, and stability of a certain stretches of amino acids (for example amino acids 20 to 50) within a protein after MDS with...
03 March 2018 274 1 View
Hi there, I have found a paper presenting results in which human cytomegalovirus load has been assessed in biopsy samples. The paper did not mentioned whether the samples were paraffin-fixed or...
02 February 2018 4,115 3 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...
01 January 2018 9,740 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...
11 November 2017 6,260 4 View
Hi there, I have recently assembled a NGS data and to see if it is currect, a company has assembled it for me. Two results are 99% identical with e-value of 0. However, I have almost 4kb extended...
09 September 2017 9,132 4 View
Dear Researchers, Hi, How can I use clinical sample like plasma, which is tested for viral infection, in cell culture propagation?. Basically, I do know the sample is positive for virus and what...
05 May 2017 5,880 5 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...
02 February 2017 7,988 6 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...
01 January 2017 1,240 3 View
Dear researchers, Hi, I have sent a DNA sample of phage for Next Generation DNA sequencing (NGS) with HiSeq for a sequence with almost 40kbp size. The company has held the process to make sure if...
12 December 2016 2,788 11 View
Hi there, I recently purchased a lentiviral packaging system containing a mixed packaging solution comprised of three separated plasmids. I have transformed a competent DH5-alpha bacteria with...
11 November 2016 6,781 5 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...
09 September 2016 5,692 2 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...
07 July 2016 6,957 5 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
05 May 2016 2,101 4 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...
09 September 2015 9,444 3 View
Dear researchers, In a ligand-based drug discovery, in which ligands are aligned to obtain a pharmacophore a pharmacophore-fit score is obtained. When I tried to do a QSAR whit that ligands, I was...
01 January 1970 3,786 15 View
Dear researchers, I have a result regarding MDS of a receptor and its complex with a ligand. Here, the results have attached – Two pictures on the top are RMSD and Rg for receptor, and the two at...
01 January 1970 7,347 14 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 1,126 4 View
