How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How to indicate the degree of litter decomposed by microbes?

Any technique could detect the degree of litter decomposed by microbes? Or any indexes could do this job? I want to split the contribution of microbes during decomposition, so any suggestions...

23 February 2021 1,362 5 View

How to Implement Elastoplasticity in a PCL model in COMSOL Multiphysics?

I am using COMSOL Multiphysics 5.5. I am trying to simulate the tensile test of PCL scaffolds. However, regardless of the strain, I have the elastic region all the time which is not true when it...

23 February 2021 4,050 1 View

How can I improve the concentration of banana fruits extracted RNA?

Currently, I'm working with banana fruits. I've tried to do RNA extractions with different methods, and I've gotten total RNA without contamination, but I couldn't get a high concentration of...

22 February 2021 6,126 2 View

Where can I find a reliable and updated methodology related with the design of spiral heat exchangers?

I need to design an spiral heat exchanger, buy I don't know what reference or bibliography (preferably a book) should I consult in order to get an updated and reliable methodology related with...

14 February 2021 7,910 3 View

Would bisulfide sequencing result be affected if the tissue is fixed by perfusion?

I am looking into DNA methylation of mice as an aging marker along with other assays and recently I added brain IF to the list of assays. For this, I need to fix the brain by transcardial...

09 February 2021 9,012 3 View

Why E1g mode (Molybdenum disulfide) is undetectable in Raman spectroscopy?

I synthesized 1T/2H hybrid phase MoS2 on a graphite foil surface by hydrothermal method, and then analyzed it by Raman spectroscopy. As a result, three new peaks correspond to the 1T phase were...

04 February 2021 6,580 2 View

Can a mRNA be degraded but still observe a protein over-expression?

Hello there, I'm currently trying to over-express a gene by transfecting the cells with a pcDNA6 plasmid containing my target gene. When I measure the mRNA for my gene of interest, the levels are...

03 February 2021 4,112 4 View

Can I use 500ng of DNA for restriction digestion?

The recommended amount of DNA for restriction digestion is 1ug in a 50ul rx I've got around 500-600ng of DNA in a total volume of 35ul. Would I get satisfactory results with this amount of DNA for...

31 January 2021 729 6 View

Difficulties purifying Outer Membrane Vesicles using a Sucrose Density Gradient: Unable to detect any protein after this process?

I'm currently trying to purify Outer Membrane Vesicles (OMVs) following their extraction from the bacteria I'm working with. After the initial extraction the concentration of protein seems good...

27 January 2021 6,852 3 View

Does increasing the number of individuals by copy-paste of the same indvs to perform GWAS affect the results?

I am trying to perform a genome-wide association on mitogenome variants (obtained from GATK-Mutect2) vs. phenotypes by using GAPIT. The number of individuals is seven and GAPIT function does not...

14 December 2020 8,853 3 View

Is there any tool to extract phenotypes from facial photos?

The facial photos corresponds to various rare genetic disorders.

22 November 2020 738 1 View

What statistical approach should I use for QTL-mapping of traits that are non-normally distributed and dependent?

Dear all, I have a genetic map constructed for the F2 cross and a corresponding phenotype data for parents and progeny. The problem with the phenotype data (it is the measurements of 5 biochemical...

10 September 2020 8,712 6 View

What is the best available software for HPO similarity measurement?

I would like to compare similarities of different allelic disorders based on HPO terms. As a first approach I just would like to select a few genes and look at how similar are the defined allelic...

10 September 2020 5,032 3 View

What systematic experiment will help determine whether or not a range of mutants with similar phenotype are derived from a common ancestor-cultivar?

Several soybean cultivars were mutagenized to produce many lines of M0, M1, M2 etc. In order to determine the genetic basis of an observed phenotype, an M0 level mutant was hybridized with its...

09 August 2020 9,224 3 View

TRP1 deficient yeast strain not growing on 5FAA containing medium?

05 August 2020 3,010 5 View

How can we perform a GWAS analysis of a qualitative trait through GAPIT?

Hi,I am doing GWAS analysis on both quantitative and qualitative trait through GAPIT 3.0. Code run well for Quantitative traits but shows following error in qualitative trait Error in...

18 July 2020 9,541 5 View

Is there any minimum sample size required for GWAS?

I am investigating on SNP-trait association in a species with a narrow genetic base. I have phenotyped and genotyped 80 accessions. I would like to use GWAS for the association analysis. From...

04 July 2020 850 9 View

How can I merge two PED/MAP file sets from different chromosome builds for GWAS study in PLINK?

Hi, I have two data sets from the illumina omniexpress snp array platform. The first data set was mapped using the GRCh37 build and the second one was more recently read using the GRCh38 build....

14 June 2020 6,281 1 View

Can someone please help with inputting PLINK assoc.logistic output files into METAL to perform a meta-analysis?

I need to perform a meta-analysis of 2 GWAS studies and I need assistance with the input study files (plink --assoc.logistic) as well as the output meta-analysis file (.TBL). - Firstly, I am not...

07 June 2020 5,831 1 View