How to build a Jupyter Notebook page to access remote Molecular Dynamics results?

Hi all, I am hoping for some assistance. I (the researcher) would like to know whether it is possible and how to go about building a Jupyter Notebook that a collaborator could load in their web...

26 January 2021 1,027 1 View

Autodock Raccoon - the following maps are missing?

I've generated a set of maps for my receptor using ADT (AutoDockTools). It has resulted in the files: .A.map .C.map .HD.map .N.map .NA.map .OA.map .SA.map .d.map .e.map But when I try loading the...

20 December 2020 7,721 2 View

How to specify binding sites in AutoDock Raccoon?

Hi all, There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result. This is concerning Raccoon(1) original, not Raccoon2. The original...

17 December 2020 4,302 2 View

How to run AutoDockTool's Autogrid4 command?

Hi all, Please imagine this to be a brand new machine with the latest installation of: Autodock Vina Autodock AutodockTools (MGLTools). I'm following a Nature Protocol for the prediction of...

14 December 2020 2,191 3 View

How do I retrieve every CID from pubchem?

Hi all, I guess there are probably several ways of doing this. I'm looking to get access to every Pubchem CID. All compounds are published for download, but the files are quite large in size and...

01 November 2020 8,612 3 View

Platelet Counting on Flow Cytometry?

Hi, Does anyone have a method for counting platelets on flow cytometry (cytometer=Cytoflex) without the need of using TRUcount beads or reference beads? Is it possible or do I need to purchase...

23 September 2020 3,509 1 View

How to get hydrogen bond analysis using MDAnalysis working with custom atom names?

Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong. I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond...

10 January 2020 7,505 6 View

How to resolve GROMACS mdrun seg fault during minimisation?

I'm waiting on email conformation for the GMX user group, but this is in reply to Reviewers so I'm pressed for time and asking here. I'm building a small collagen-based system. The crystal...

13 November 2019 5,517 10 View

Are these QC DFT settings appropriate?

I'm picking up quantum chemistry after a three year break. I've forgot a lot and I'm now using ORCA (version 4.0.1.2). My system is a non-enzymatic chemical reaction between lysine, arginine...

30 August 2019 3,966 2 View

How to calculate whether a disease outcome in a population is by chance or significant?

Hello all, I have a huge dataset of longitudinal medical records. Each record contains indications for drug and disease. I have been able to calculate the Cure Rate in the population given a...

04 October 2018 2,529 3 View

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02 March 2021 3,060 3 View

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View

Issues with Permeabilization during Flow Cytometry?

Hello Everyone. Currently I am working to characterize macrophages in the myocardium after ischemia-reperfusion injury in rats. Due to the low total cell number isolated from rat hearts I can...

01 March 2021 3,867 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

How to check the uv-vis absorption of nanoparticle by surface plasmon resonance?

I try to check the uv-vis absorption of Indium nanoparticle. Now I am measuring in solution, can I measure it in the form of a film?

01 March 2021 930 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

What could be some reasons why unstimulated monocytes are getting activated?

Im doing PBMC isolation -> CD14+ enrichment using magnetic beads -> stimulation setup. My negative control is just cells in cRPMI but they seem to get activated over and over again.

28 February 2021 7,883 3 View

RIA. How to measure?

When you use RIA, with a control the unknown sample with antibodies, you bare in mind the binding sites of the antibodies. However you still need to measure labelled antigen (radioactive) and not...

28 February 2021 2,133 3 View