In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?
I have a dataset with about 80 different species. As usual, some species are very easy to identify with certainty whereas others are more difficult, which means that I am less certain of my...
03 March 2021 8,066 4 View
I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...
02 March 2021 1,830 3 View
Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue
02 March 2021 5,433 5 View
I have an input video, of skin (from a microscope that means it is magnified such that blood capillaries are visible). The idea is to extract 15 sec of continuous frames from a video of 1 min,...
02 March 2021 2,735 2 View
Hello, I would like to ask how to grow E.coli which resists 50 or 100ug/ml of Blasticidin. I have tried many methods by using low salt Luria-Bertain(LB) agar plate. However, no colonies grow. Let...
01 March 2021 2,027 2 View
I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...
01 March 2021 4,128 3 View
I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??
28 February 2021 2,153 1 View
Favourable conditions of base pressure, rate of deposition. Also, by which characterisation technique to be used to verify the thickness of the deposited film.
28 February 2021 3,640 3 View
The following code (see 1st 2 images attached) is used to produce PID controller values that are designed to control the system (G). The code finds the PID controller values (noted as k) by using...
28 February 2021 6,560 14 View
Hi everybody, I have been running a multiplex IHC which allow me to stain the same tissue with different markers (Primary Ab + Secondary conjugated Ab) (AF487, AF555, AF647). Since I would like to...
27 February 2021 5,028 2 View
I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...
19 February 2021 1,236 1 View
I am new to Docking and MD, and currently try to catch on it. I try one of the webserver for docking, but unfortunately not working. it says " Your PDB contains multiple forms of the same residue...
08 February 2021 7,426 3 View
I have a trajectory file of about 1000 frames which I have calculated a center of mass for each frame. I would like to use the first frame as a reference and see how much the center of mass...
04 February 2021 5,774 1 View
I used autodock to complete the docking between the ligand and the protein. I have a question, why the dimension of the result after docking is much smaller than the dimension of the protein...
24 January 2021 7,363 3 View
I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...
19 January 2021 531 3 View
Hi. I'm using the PyRx version 0.8 and getting the error message: WARNING: Filename mismatch: "2DFN_ADP_CL.maps.fld" :: "..\2DFN_ADP_CL.maps.fld" C:\Program Files (x86)\The Scripps Research...
17 January 2021 843 3 View
Hello everyone, I would like to get help about finding any server or application which can give me info about free energy and dissociation constant of protein-protein docking outputs. I have...
15 January 2021 587 3 View
I have been using PyRx to dock peptides to a protein. Initially the numbers were small so it was okay. But now I have to dock over 500 peptides and doing so manually would take forever. My...
10 January 2021 3,330 4 View
I have been processing some trajectory files from my molecular dynamics simulation using GROMACS by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein...
30 December 2020 849 4 View
I have used Autodock 4.2 for docking studies and trying haddock for DNA-Ligand docking. It shows an error and not supported DNA PDB file. Suggest a template for DNA and ligand PDB file and also...
29 December 2020 1,322 8 View