ARAP interpolation for protein structures

Hi everyone, In this post, I will show you how to use the ARAP Path Element for generating a path between two protein structures. Let us start with a list of requirements, then a tutorial on how to use the app. Requirements SAMSON version 0.7.0 or higher ARAP Path app Before starting the tutorial, I would like to ask you to download this file (ArapInterpolation) which contains necessary files for this tutorial. After extracting it, you will have two pdb…

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Ligand unbinding pathway search

Hi everyone, In this post, I will show you how to use the Ligand Unbinding Pathway Search app for finding possible ligand unbinding pathways from a protein. Let us start with a list of requirements, and then a tutorial on how to use the app. Requirements SAMSON 0.7.0 The Ligand Unbinding Pathway Search app The GROMACS force field interaction model The FIRE state updater Before starting the tutorial, I would like to ask you to download this file (LigandUnbindingPathSearch) which…

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Protein conformational transition search

Hi everyone, In this post, I will show you how to use the Protein Conformational Transition Search app for finding possible paths between two conformations of a protein. Let us start with a list of requirements, and then a tutorial on how to use the app. Requirements SAMSON 0.7.0 Protein Conformational Transition Search app GROMACS force field interaction model FIRE state updater Before starting the tutorial, I would like to ask you to download this file (ProteinPathSearch) which contains necessary…

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