Minh Khoa Nguyen

ARAP interpolation for protein structures

Minh Khoa Nguyen July 24, 2018 May 25, 2020

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…

More…

Ligand unbinding pathway search

Minh Khoa Nguyen July 4, 2018 May 25, 2020

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…

More…

Protein conformational transition search

Minh Khoa Nguyen July 3, 2018 May 25, 2020

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…

More…