Author: Dmitriy Marin

In this tutorial, we will show you how to use the Interactive Ramachandran Plot SAMSON extension. First, go to SAMSON Extensions web page, log in, and add the Interactive Ramachandran Plot SAMSON extension. The Ramachandran plot is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. For this tutorial, you can open any protein you like. We will be using 1YRF. You can use the Protein Data Bank Downloader to fetch molecules from…

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In this tutorial, you will learn how to perform covalent and non-covalent protein-ligand docking with the FITTED Suite SAMSON Extension. The FITTED Suite SAMSON Extension was done in partnership with Molecular Forecaster and wraps their Fitted Docking software. FITTED stands for Flexibility Induced Through Targeted Evolutionary Description. This fully automated docking software is unique in that it considers the flexibility of macromolecules, the presence of bridging “displaceable” water molecules, covalent functional groups, and proton shifts upon metal coordination. FITTED is…

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In this tutorial, we will show how to export atoms positions (for all atoms in the system or for a selection of atoms) along paths in PDB files thanks to the Export Along Paths app. This could be useful for example if you want to generate reaction coordinates for free energy calculations.   Requirements Export Along Paths Extension Before starting the tutorial, please download the 1pv7_ligand_complex_with_paths (~13 MB) which contains files for this tutorial. Tutorial Launch SAMSON. Load 1pv7_ligand_complex_with_paths.sam file…

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The Nudged Elastic Band (NEB) method allows for finding saddle points and minimum energy paths between known conformations. The method optimizes a number of intermediate images along the path by finding the lowest possible energy for each image while maintaining equal spacing between neighboring images. This constrained optimization is done by adding spring forces. The NEB method can be used, for example, to determine transition paths between already obtained structures corresponding to local energy minima (obtained using, e.g., the FIRE…

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In this post, we will show how to use the Protein Path Finder app for finding possible paths between two conformations of a protein. Content Requirements Tutorial Loading the input model Launching the Protein Path Finder app Setting up the interaction model and the state updater for energy evaluation Setting up the system Defining the sampling box Defining the parameters Running, pausing, or stopping the planner Results Next steps Creating pathlines Improving paths with P-NEB Exporting atoms trajectories along paths…

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In this post, we will show how to use the Ligand Path Finder app for finding possible ligand unbinding pathways from a protein. Content Requirements Tutorial Loading the input model Launching the Ligand Path Finder app Setting up the interaction model and the state updater for energy evaluation Setting up the system Defining the sampling box Defining the parameters Running, pausing, or stopping the planner Results Next steps Creating pathlines Improving paths with P-NEB Exporting atoms trajectories along paths Requirements…

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In this post, we will show you how to create pathlines thanks to the Pathlines visual model. Pathlines are visual models which represent the trajectory of the center of mass of selected atoms along selected Paths. Pathlines may be used to understand the motion of a single atom, or a group of atoms, along a path/trajectory. Before starting the tutorial, please, download this archive: Pathlines (~13MB). It contains a file (1pv7_ligand_complex_with_paths.sam) from the Ligand Path Finder tutorial with already computed…

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