How to read Gaussian Cube file?

Hi, I have a Gaussian cube file (.cube) that I obtained with gmx spatial. It represents the spatial density of cholesterol during a simulation (Protein in a membrane with explicit solvent). I...

03 April 2019 9,161 1 View

How to calculate the tilt angle of a protein (or a helix) with respect to the membrane plane?

Hi, I have a Coarse-grained simulation of a dimer with 5 transmembrane helices for each monomer and I would like to calculate the tilt angle of each monomer with the respect to the membrane...

31 December 2018 5,872 2 View

How to quantify the arrangement between helices during MD and also the effect of CHOL on the conformational changes of certain helices?

Dears, I run several Coarse grained simulations of a transmembrane protein using Martini FF. In order to do a deep analysis of my systems, I backmapped a part of the trajectory from CG to AA....

09 October 2018 4,361 2 View

How to estimate the loss in helix during MD simulation?

Dears, I run MD simulation on a transmembrane protein. When I visualised the frames, it seemed that I have some loss in alpha-helix (TM region). How can I quantify this? NB: I used timeline of...

07 August 2018 4,157 4 View

What is the lipid composition of the mitochondrial Outer Membrane (omm)?

Dear all, I would like to simulate a protein which is located in the Mitochondrial Outer Membrane (OMM). I was searching in the literature about lipid composition of this latter (in Mammals) but...

01 February 2018 5,040 2 View

How to analyzing Desmond trajectories using GROMACS tools?

02 March 2017 964 2 View

What kind of analyses that can be performed on a protein in order to study differences petween the apo and holo form during MD simulation?

10 November 2016 8,125 5 View

How to generate a topology for a HEM protein using CHARMM 27 as FF?

Dear all, I'm working on simulating a homodimer with its cofactors (hem, THG) and its substrate with GROMACS. Since my system is complex, I decided to start first with a monomere taking only...

04 May 2016 637 2 View

Fixing missing atoms and residues in PDB file before using pdb2gmx

Hello, I have missing atoms and residues in my PDB file and I need to fix them in order to proceed with pdb2gmx (GROMACS). I used swissModel but the generating file is lacking the final residue in...

04 May 2016 7,450 6 View

implication of inflamatory proteins in systemic sclerosis

04 May 2011 8,336 0 View

Which of the Covid-19 Vaccines would elicit the best immunoprotection and why?

I want to know which of the available Covid-19 Vaccines would elicit the best immunological response and why

02 March 2021 1,388 3 View

Experimental Design: How deal with pseudreplicates with immunological and clinical-chemical paramaeters?

Hello everybody, I am investigating the influence of a toxinon various clinical-chemical and haematological parameters in fish. I have three treatments (control, low dose, high dose) in my...

24 February 2021 1,243 1 View

Looking for advices and tips to improve the staining and the gating strategy in human blood?

Hi, I am staining a human blood with CD19, CD3,CD14 and CD16. My gating strategy in FlowJo goes like this: - First, I gate a general population SSC-A VS FSC-A => Then gate for single cells, =>...

21 February 2021 5,724 4 View

Can you polarize Jurkat cells into different T helper subsets?

I am wondering if anyone has had success with in vitro polarization (via cytokines) of Jurkat cells. My goal is to understand the affect of a drug on Treg induction and differentiation. I...

12 January 2021 3,606 2 View

Can only the spike protein of the virus provide immunity?

Virology, microbiology, immunology, vaccine

21 December 2020 424 16 View

Can somebody recommend me a decent textbook to learn more about signaling pathways and their mechanistic principles in general?

I studied biochemistry and molecular biology in my bachelors and Immunology in my masters. I never came across a suitable course for general signaling pathways and principles. My interest is...

13 December 2020 5,690 5 View

Is it possible to extract DNA or RNA from paraffinized biopsies ?

My lab have some skin biopsies that were previously conserved in paraffine , and i wanted to know if it is possible to extract DNA or RNA from them.

06 December 2020 7,964 6 View

Could the desmin mutation in myofibrillar myopathy be caused by an infection?

A patient with desminopathy (mutation Thr341Pro DES in a heterozygous state) with the progression of the disease has a decrease in taste and smell, immunosuppression, and an increase in IgA in the...

02 November 2020 5,886 6 View

Whis HLA-A2 TAAs are best for DC pulsation and CD8+ cytotoxic T cell induction?

When looking to establish Ag-specific CD8 cytotoxic T cells with autologous dendritic cells, there are numerous tumor-associated Ags to choose from. Does anybody know which Ags give the best...

27 October 2020 2,068 2 View

Resuspending cell pellet after ficoll centrifugation?

In my current project I am planning to isolate mononuclear cells from peritoneal ascites of cancer patients using ficoll centrifugation. However, following isolation of the mononuclear cell layer,...

26 October 2020 5,966 4 View