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Detect amino acid interactions

Updated: January 3, 2022

You want to study the specific interactions between a protein and a small peptide. In this recipe we are going to use the system published by Mudd and collaborators which consists of an enzyme (receptor tyrosine kinase) and… Read More

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Making a 3d histogram of the position of a small molecule around a receptor.

Updated: January 1, 2022

You want to see where a ligand is spending more time around a receptor. When you have a ligand that is exploring multiple binding positions, sometimes is useful to visually see where it is spending more time. A… Read More

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Hydrogen bond analysis between a protein and a small molecule

Updated: April 12, 2023

You want to study the hydrogen bonds between a small molecule and a protein. We can use the hbond command that will use a geometric consideration (distance of 3.0 Å and an angle cutoff of 135°) to consider… Read More

Category: Uncategorized