How to prepare protein-ligand complex pdb for generating 2-D figure in LigPlot?

I have a pdb file of docked complex of protein and ligand from patchdock, but there is an error occurring when I am importing it to LigPlot.

01 February 2019 2,724 10 View

How to implement neomodal driver of python to implement neo4j database in my local website?

I need to integrate an existing neo4j-database into my django project using your package. Is there any best practice or things I need to consider to do this?

10 November 2018 9,306 0 View

What are the way to retrive data from different columns of existing tables in database by selecting checkbox through php?

I have a multiple checkbox (about 40) in search form of my website. This checkbox contain names of tables stored in database. I am unable to fetch data from columns of the tables in database by...

07 August 2018 4,176 1 View

How to implement graph network built on neo4j browser into our locally built website?

I built a network graph between RBP and non coding element on the basis of positive and negative value of correlation which is statistical parameter on neo4j browser. I just want to impliment this...

07 August 2018 4,494 2 View

How to retrive multiple data stored in database using checkbox through php?

I made a website where in my search page. I gave checkbox option to retrive data which are stored in our database. when I click on multiple checkbox, I am unable to find the result. what can I do,...

07 August 2018 4,769 3 View

Anyone please tell me how to built RBP-miRNA interaction regulome model?

Q-How can we construct RBP-miRNA interaction base gene expression regulatory network from CLIP-seq ,RNA-seq and miRNA seq data?

05 June 2018 4,902 4 View

How to write cypher query for neo4j graph database of my sample data file containing 7 different column ?

I have a sample data file which contain following data: hsa-miR-101-3p hsa-mir-101-2 AGO1 AGO2 NA NA NA hsa-miR-101-3p hsa-mir-101-2 AGO1 AGO3 NA NA NA hsa-miR-101-3p hsa-mir-101-2 AGO1 AGO4 NA...

05 June 2018 8,929 1 View

How do I run a Python script on my web server?

06 July 2017 7,836 1 View

What is the reson for descripancy found in evaluatric parameter for built model?

02 March 2017 9,083 0 View

What is the best tool for pattern recognition of image data for applying svm?

Can anyone suggest me which machine learning tool are best for applying SVM techniques for pattern recognition from image data

05 June 2016 6,937 12 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

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

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View

RNA degraded after good nanodrop readings?

23 February 2021 8,850 2 View