Why when I try to refine the structure of a peptide with Xplor-NIH the following error occurs?

annealtt.py(48): protocol.genExtendedStructure() fixupCovalentGeom: Covalent geometry still violated at exit. ........ As a result, some angles and dihedrals are violated, and structures are not...

08 September 2018 8,596 0 View

Why LTOD patch, deform the structure of aromatics rings...?

I'm building a psf for Xplor, I use LTOD patch to change L-proline to D in a peptide, but when I visualize the structure in VMD, the rings of PHE and TYR deform...That is absurd, because the patch...

03 April 2018 8,300 0 View

During an MD simulation the disulfide bonds are increasing over time, can someone help us with this?

We are doing a molecular dynamic simulation with GROMACS using the AMBER force field. During the simulation the disulfide bonds are increasing over time. We set the bridge manually with pdb2gmx...

05 June 2015 5,689 3 View

Why does blocking with my immunogenic peptide cause nuclear fluorescence in ICC?

Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...

03 March 2021 5,999 3 View

How do I determine the degree of polymerization of PEG 400 based on NMR integration?

Hello, I am working on the photocatalytic degradation of PEG 400. I would like to know if it's possible to determine the degree on polymerization based on NMR integration, or by the MW of the...

02 March 2021 6,186 3 View

Do you know any MR image dataset?

I would like to research on MR images (0.5T and 3T). Can you please suggest some websites that I can download dataset including both 0.5T and 3T MR images? Thank you.

02 March 2021 7,735 3 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

Does the circuit modeling for planar monopole antennas using Foster canonical forms give good approximation?

Hi researchers, I am searching for some accurate way to do the circuit modeling of planar CPW-fed monopole antennas. I have gone through the literature where mostly circuit modeling is done using...

28 February 2021 7,016 1 View

How to include original NMR data in a manuscript?

hello. i am junior researcher. I received a comment from a reviewer that he could not find NMR data in my submitted paper. I had included the NMR graph with explanation and formula to calculate...

27 February 2021 734 4 View

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23 February 2021 4,014 3 View

How to reduce static electricity of powder after lyophilization?

I am working on synthesizing and then purifying peptides using the SPPS system. After purification of the peptide, the peptide powder is obtained using a freeze dryer. When measuring the powder,...

22 February 2021 10,099 5 View

Can we remove the fmoc group after peptide cleavage?

I have synthesized the peptide using Fmoc based solid phase peptide synthesis. Also I have cleaved the peptide from the resin and lyophilized it, but later realized that, I forgot to deprotect the...

21 February 2021 4,537 3 View

How T cells recognise non-peptide antigens?

This might sound very basic question, but please share with me an explanation of how the T cell is activated when the antigen is not a peptide? What happens? And what are the molecules involved in...

21 February 2021 564 3 View