Antibody amino acid sequence database to simulation?

Hello, I need your help. I am looking for a database of antibody amino acid sequences for later simulation in a program in order to analyze their structure. The antibodies I need to test...

18 February 2021 371 4 View

How long can we consider that the data obtained with qualitative social research methods are "current"?

I cannot find any reference that deals with the temporal validity of qualitative data. I think there is a gap in the methodological literature on the temporal validity of the research results and,...

05 February 2021 9,788 20 View

Does DNA A-tailing survive after agarose gel electrophoresis and purification?

Hi everyone, I need to clone in pGEM-T vector the result of amplifying a metagenomic library by PCR with a high fidelity polymerase but I only want to clone the fragments of an specific size...

04 February 2021 6,051 8 View

How can I solve this problem with agarose gel DNA purification of bigger (1-4kb) fragments ?

Hi everyone, I perform a PCR + Restriction Digestion (single cut, same at both sides) over a metagenomic library. After that, I am trying to purifiy DNA fragments between 1-4kbp long from the...

24 January 2021 2,190 5 View

What is the most adequate (serum) dilution to use to determine IgE in mice serum via ELISA assay (commercial kit)?

We have a commercial kit from RayBioTech to determine IgE from mice serum. In accordance with the supplier's instructions, we have to use a dilution of 1:10000 of the serum. Is this dilution the...

06 January 2021 4,217 3 View

Is there any reference levels of IgE in healthy mice serum, like there are for other biochemical processes/components?

My question goes for reference levels of IgE in mice serum. I know that there are tables for the most common biochemical processes/compounds (red blood cells, white blood cells, AST, ALT, etc),...

06 January 2021 8,215 3 View

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It is important for me to know the opinion from your point of view as researchers.

30 December 2020 988 2 View

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13 December 2020 3,861 3 View

How can I do the bang's blinding index and james blinding index?

Hi! I would like to know with which statistical software the bang blinding index and the James blinding index and how to do it. Thanks

09 December 2020 1,363 2 View

Do anyone know a lab in Mexico where dielectric properties of solids and liquid can be measured?

I mean those kits that can be connected to vector network analyzers in order to find out permittivity and permeabilitty of solid and liquid from around 1 to 10 or 30 GHz

25 November 2020 852 1 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Can we incorporate unnatural amino acids into protein using software for graphical image purpose?

I am looking to incorporate a unnatural amino acids which is not available in the swisssidechain database into a protein crystal structure of pdb? I am using chimera 1.14 vis. tool?

26 January 2021 4,064 3 View

How to phosphorylate specific residues on pymol?

Hi everyone, I am using the pyTMs plug in on Pymol to phosphorylate a particular threonine in my protein. I am having difficulty in selecting only one or two residues - it seems I can only...

05 January 2021 230 3 View

How to interpret Energy minimization results?

I have conducted an EM using YASARA server, and the output PDB is viewed in PyMol to understand the conformational changes between model that is energy minimized and the original model. I have...

28 December 2020 2,029 2 View

How can I use the selection matrix in Pymol to select atoms by their number within a cofactor?

I work with photochemical reaction centers (like Photosystems I & II) and it can be helpful to use PyMol to create useful pictures of them. With these proteins, the chlorophylls do all the...

04 December 2020 4,778 2 View

How can I build a membrane patch with multiple monomers of a peptide?

Hi, I have been looking around for ways to insert various monomers of an AMP in membrane bilayers. To start-off, I have been using Charm-Gui, but it seems that I can only insert one peptide at a...

29 November 2020 8,660 2 View

Parsing error in autodock vina?

I'm trying to use autodock vina, and I received the following error for the ligand file when running the configuration: "Parse error on line 26 in file "15.pdbqt": Unknown or inappropriate...

21 October 2020 7,245 1 View

How to convert Gro files to Pdb using gromacs?

Hello, After I minimized the protein structure I used editconf in gromacs to convert the minimized GRO file to PDB. when I visualized the PDB file produced, it was totally corrupted which...

09 October 2020 547 4 View

How can I add a chain identifier to a PDB file generated by Phyre2?

I am trying to use DynaMut2 to study stabilizing/destabilizing effects of mutations in a protein. I generated a 3D structure using Phyre2, and it gave me a PDB file without a chain identifier....

22 September 2020 495 11 View

Does anyone has achieved the installation of gromacs plugin in PyMol, complete in Linux, with its graphic interface?

I am using Ubuntu 20.04 and I have PyMol installed, with a license. But it has been impossible to add the repository ppa:makson96/dynamics. Even downloaded from github, the package with the...

20 September 2020 6,870 1 View