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- learn how to calibrate NOE data to obtain distance restraints,
- derive a protein structure with the software CYANA,
- try how the exchange of the ligand between free and bound state influence the NOESY spectra,
- derive the structure of protein-ligand complex,
- try how the incomplete assignment due to chemically identical atoms affect the NOESY simulation.
Instructions:
- download exercises.tgz, for example, to Documents, and unpack them (in console/terminal, execute: cd Documents; tar xzvf exercises.tgz).
- download the pythonScripts.tgz, if you wish to do the calculations yourself (many are time consuming).
- place the python directory, e.g., to the bin folder. In steps: create by mkdir bin, then, if the scripts were in the Downloads folder, use mv Downloads/python.tgz bin; cd bin; tar xzvf python.tgz, and ensure that the bin/python is in the $PYTHONPATH:
- in terminal, execute: export PYTHONPATH=$PYTHONPATH:$HOME/bin/python
- lecture slides presentation.pdf
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module add vmd
Lecture slides can be downloaded here: presentation.pdf
At wolf.ncbr.muni.cz, paste these command to the terminal/console and press enter (for other machine, follow the instructions at the end of the page).
module add vmd
export PYTHONPATH=$PYTHONPATH:/home/schools/25-02-ML4NGP/bin/python
export PATH=/home/schools/25-02-ML4NGP/bin/cyana-3.98.15JO:/home/schools/25-02-ML4NGP/bin/python:$PATH
module add
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anaconda3:2024.02
conda init
source .bashrc
conda activate base
cp /home/schools/25-02-ML4NGP/NOE/exercises.tgz .
tar xzvf exercises.tgz
cd exercises
Introduction for Task 1:
In real experimental situation, we have never complete set of distances between each pair of protons. The NOE crosspeaks are detectable for distances up to around 5 Angstrom. From these, many signal would share the
same frequency in the spectrum, and thus, assignment between signal and atom (atom pair) can be done only within some group, or not at all. Furthermore, the experimentally-derived distances contain various sources of error.
Partly, it is due to random noise, but partly due to incompletely resolved relayed transfer and partly due to different (local) dynamics influencing the cross-relaxation rate.
Let's start anyway with the unrealistic situation, where we know all the distances within 5.5 A, accurately.
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- What is the difference WRT 040 ?
Instructions at different machine:
- download exercises.tgz, for example, to Documents, and unpack them (in console/terminal, execute: cd Documents; tar xzvf exercises.tgz).
- download the pythonScripts.tgz, if you wish to do the calculations yourself (many are time consuming).
- place the python directory, e.g., to the bin folder. In steps: create by mkdir bin, then, if the scripts were in the Downloads folder, use mv Downloads/python.tgz bin; cd bin; tar xzvf python.tgz, and ensure that the bin/python is in the $PYTHONPATH:
- in terminal, execute: export PYTHONPATH=$PYTHONPATH:$HOME/bin/python
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Prepared by Dr. Jiří Mareš,shaped by discussion with Prof. Julien Orts, Florian Wolf M.Sc. and other members of the research group (https://bionmr.univie.ac.at/people/)
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